1
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Bommisetti P, Bandarian V. Insights into the Mechanism of Installation of 5-Carboxymethylaminomethyl Uridine Hypermodification by tRNA-Modifying Enzymes MnmE and MnmG. J Am Chem Soc 2023; 145:26947-26961. [PMID: 38050996 PMCID: PMC10723064 DOI: 10.1021/jacs.3c10182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 11/20/2023] [Accepted: 11/22/2023] [Indexed: 12/07/2023]
Abstract
The evolutionarily conserved bacterial proteins MnmE and MnmG (and their homologues in Eukarya) install a 5-carboxymethylaminomethyl (cmnm5) or a 5-taurinomethyl (τm5) group onto wobble uridines of several tRNA species. The Escherichia coli MnmE binds guanosine-5'-triphosphate (GTP) and methylenetetrahydrofolate (CH2THF), while MnmG binds flavin adenine dinucleotide (FAD) and a reduced nicotinamide adenine dinucleotide (NADH). Together with glycine, MnmEG catalyzes the installation of cmnm5 in a reaction that also requires hydrolysis of GTP. In this letter, we investigated key steps of the MnmEG reaction using a combination of biochemical techniques. We show multiple lines of evidence supporting flavin-iminium FADH[N5═CH2]+ as a central intermediate in the MnmEG reaction. Using a synthetic FADH[N5═CD2]+ analogue, the intermediacy of the FAD in the transfer of the methylene group from CH2THF to the C5 position of U34 was unambiguously demonstrated. Further, MnmEG reactions containing the deuterated flavin-iminium intermediate and alternate nucleophiles such as taurine and ammonia also led to the formation of the anticipated U34-modified tRNAs, showing FAD[N5═CH2]+ as the universal intermediate for all MnmEG homologues. Additionally, an RNA-protein complex stable to urea-denaturing polyacrylamide gel electrophoresis was identified. Studies involving a series of nuclease (RNase T1) and protease (trypsin) digestions along with reverse transcription experiments suggest that the complex may be noncovalent. While the conserved MnmG cysteine C47 and C277 mutant variants were shown to reduce FAD, they were unable to promote the modified tRNA formation. Overall, this study provides critical insights into the biochemical mechanism underlying tRNA modification by the MnmEG.
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Affiliation(s)
- Praneeth Bommisetti
- Department of Chemistry, University of Utah, Salt Lake
City, Utah 84112, United States
| | - Vahe Bandarian
- Department of Chemistry, University of Utah, Salt Lake
City, Utah 84112, United States
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2
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Gerson TM, Ott AM, Karney MMA, Socea JN, Ginete DR, Iyer LM, Aravind L, Gary RK, Wing HJ. VirB, a key transcriptional regulator of Shigella virulence, requires a CTP ligand for its regulatory activities. mBio 2023; 14:e0151923. [PMID: 37728345 PMCID: PMC10653881 DOI: 10.1128/mbio.01519-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 07/25/2023] [Indexed: 09/21/2023] Open
Abstract
IMPORTANCE Shigella species cause bacillary dysentery, the second leading cause of diarrheal deaths worldwide. There is a pressing need to identify novel molecular drug targets. Shigella virulence phenotypes are controlled by the transcriptional regulator, VirB. We show that VirB belongs to a fast-evolving, plasmid-borne clade of the ParB superfamily, which has diverged from versions with a distinct cellular role-DNA partitioning. We report that, like classic members of the ParB family, VirB binds a highly unusual ligand, CTP. Mutants predicted to be defective in CTP binding are compromised in a variety of virulence attributes controlled by VirB, likely because these mutants cannot engage DNA. This study (i) reveals that VirB binds CTP, (ii) provides a link between VirB-CTP interactions and Shigella virulence phenotypes, (iii) provides new insight into VirB-CTP-DNA interactions, and (iv) broadens our understanding of the ParB superfamily, a group of bacterial proteins that play critical roles in many bacteria.
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Affiliation(s)
- Taylor M. Gerson
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, USA
| | - Audrey M. Ott
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, USA
| | - Monika M. A. Karney
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, USA
| | - Jillian N. Socea
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, USA
| | - Daren R. Ginete
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, USA
| | | | - L. Aravind
- Computational Biology Branch, National Library of Medicine, Bethesda, Maryland, USA
| | - Ronald K. Gary
- Department of Chemistry and Biochemistry, University of Nevada Las Vegas, Las Vegas, Nevada, USA
| | - Helen J. Wing
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, USA
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3
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Gerson TM, Ott AM, Karney MMA, Socea JN, Ginete DR, Iyer LM, Aravind L, Gary RK, Wing HJ. VirB, a key transcriptional regulator of Shigella virulence, requires a CTP ligand for its regulatory activities. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.16.541010. [PMID: 37293012 PMCID: PMC10245682 DOI: 10.1101/2023.05.16.541010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The VirB protein, encoded by the large virulence plasmid of Shigella spp., is a key transcriptional regulator of virulence genes. Without a functional virB gene, Shigella cells are avirulent. On the virulence plasmid, VirB functions to offset transcriptional silencing mediated by the nucleoid structuring protein, H-NS, which binds and sequesters AT-rich DNA, making it inaccessible for gene expression. Thus, gaining a mechanistic understanding of how VirB counters H-NS-mediated silencing is of considerable interest. VirB is unusual in that it does not resemble classic transcription factors. Instead, its closest relatives are found in the ParB superfamily, where the best-characterized members function in faithful DNA segregation before cell division. Here, we show that VirB is a fast-evolving member of this superfamily and report for the first time that the VirB protein binds a highly unusual ligand, CTP. VirB binds this nucleoside triphosphate preferentially and with specificity. Based on alignments with the best-characterized members of the ParB family, we identify amino acids of VirB likely to bind CTP. Substitutions in these residues disrupt several well-documented activities of VirB, including its anti-silencing activity at a VirB-dependent promoter, its role in generating a Congo red positive phenotype in Shigella , and the ability of the VirB protein to form foci in the bacterial cytoplasm when fused to GFP. Thus, this work is the first to show that VirB is a bona fide CTP-binding protein and links Shigella virulence phenotypes to the nucleoside triphosphate, CTP. Importance Shigella species cause bacillary dysentery (shigellosis), the second leading cause of diarrheal deaths worldwide. With growing antibiotic resistance, there is a pressing need to identify novel molecular drug targets. Shigella virulence phenotypes are controlled by the transcriptional regulator, VirB. We show that VirB belongs to a fast-evolving, primarily plasmid-borne clade of the ParB superfamily, which has diverged from versions that have a distinct cellular role - DNA partitioning. We are the first to report that, like classic members of the ParB family, VirB binds a highly unusual ligand, CTP. Mutants predicted to be defective in CTP binding are compromised in a variety of virulence attributes controlled by VirB. This study i) reveals that VirB binds CTP, ii) provides a link between VirB-CTP interactions and Shigella virulence phenotypes, and iii) broadens our understanding of the ParB superfamily, a group of bacterial proteins that play critical roles in many different bacteria.
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Affiliation(s)
- Taylor M. Gerson
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV 89154-4004, USA
| | - Audrey M. Ott
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV 89154-4004, USA
| | - Monika MA. Karney
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV 89154-4004, USA
| | - Jillian N. Socea
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV 89154-4004, USA
| | - Daren R. Ginete
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV 89154-4004, USA
| | - Lakshminarayan M. Iyer
- Computational Biology Branch, 8600 Rockville Pike, Building 38A, Room 5N505, National Library of Medicine, Bethesda, MD 20894
| | - L. Aravind
- Computational Biology Branch, 8600 Rockville Pike, Building 38A, Room 5N505, National Library of Medicine, Bethesda, MD 20894
| | - Ronald K. Gary
- Department of Chemistry and Biochemistry, University of Nevada Las Vegas, Las Vegas, NV 89154-4003
| | - Helen J. Wing
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV 89154-4004, USA
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4
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Lyu Z, Wilson C, Ling J. Translational Fidelity during Bacterial Stresses and Host Interactions. Pathogens 2023; 12:383. [PMID: 36986305 PMCID: PMC10057733 DOI: 10.3390/pathogens12030383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 02/22/2023] [Accepted: 02/24/2023] [Indexed: 03/05/2023] Open
Abstract
Translational fidelity refers to accuracy during protein synthesis and is maintained in all three domains of life. Translational errors occur at base levels during normal conditions and may rise due to mutations or stress conditions. In this article, we review our current understanding of how translational fidelity is perturbed by various environmental stresses that bacterial pathogens encounter during host interactions. We discuss how oxidative stress, metabolic stresses, and antibiotics affect various types of translational errors and the resulting effects on stress adaption and fitness. We also discuss the roles of translational fidelity during pathogen-host interactions and the underlying mechanisms. Many of the studies covered in this review will be based on work with Salmonella enterica and Escherichia coli, but other bacterial pathogens will also be discussed.
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Affiliation(s)
| | | | - Jiqiang Ling
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, MD 20742, USA
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5
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Srimahaeak T, Thongdee N, Chittrakanwong J, Atichartpongkul S, Jaroensuk J, Phatinuwat K, Phaonakrop N, Jaresitthikunchai J, Roytrakul S, Mongkolsuk S, Fuangthong M. Pseudomonas aeruginosa GidA modulates the expression of catalases at the posttranscriptional level and plays a role in virulence. Front Microbiol 2023; 13:1079710. [PMID: 36726575 PMCID: PMC9884967 DOI: 10.3389/fmicb.2022.1079710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 12/29/2022] [Indexed: 01/19/2023] Open
Abstract
Pseudomonas aeruginosa gidA, which encodes a putative tRNA-modifying enzyme, is associated with a variety of virulence phenotypes. Here, we demonstrated that P. aeruginosa gidA is responsible for the modifications of uridine in tRNAs in vivo. Loss of gidA was found to have no impact on the mRNA levels of katA and katB, but it decreased KatA and KatB protein levels, resulting in decreased total catalase activity and a hydrogen peroxide-sensitive phenotype. Furthermore, gidA was found to affect flagella-mediated motility and biofilm formation; and it was required for the full virulence of P. aeruginosa in both Caenorhabditis elegans and macrophage models. Together, these observations reveal the posttranscriptional impact of gidA on the oxidative stress response, highlight the complexity of catalase gene expression regulation, and further support the involvement of gidA in the virulence of P. aeruginosa.
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Affiliation(s)
- Thanyaporn Srimahaeak
- Program in Applied Biological Sciences, Chulabhorn Graduate Institute, Bangkok, Thailand,Department of Biotechnology, Faculty of Engineering and Industrial Technology, Silpakorn University, Sanamchandra Palace Campus, Nakhon Pathom, Thailand
| | - Narumon Thongdee
- Program in Applied Biological Sciences, Chulabhorn Graduate Institute, Bangkok, Thailand
| | | | | | - Juthamas Jaroensuk
- Program in Applied Biological Sciences, Chulabhorn Graduate Institute, Bangkok, Thailand
| | - Kamonwan Phatinuwat
- Program in Applied Biological Sciences, Chulabhorn Graduate Institute, Bangkok, Thailand
| | - Narumon Phaonakrop
- Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Janthima Jaresitthikunchai
- Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Sittiruk Roytrakul
- Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Skorn Mongkolsuk
- Program in Applied Biological Sciences, Chulabhorn Graduate Institute, Bangkok, Thailand,Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok, Thailand,Center of Excellence on Environmental Health and Toxicology (EHT), OPS, MHESI, Bangkok, Thailand
| | - Mayuree Fuangthong
- Program in Applied Biological Sciences, Chulabhorn Graduate Institute, Bangkok, Thailand,Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok, Thailand,Center of Excellence on Environmental Health and Toxicology (EHT), OPS, MHESI, Bangkok, Thailand,*Correspondence: Mayuree Fuangthong, ✉
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6
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Bommisetti P, Young A, Bandarian V. Elucidation of the substrate of tRNA-modifying enzymes MnmEG leads to in vitro reconstitution of an evolutionarily conserved uridine hypermodification. J Biol Chem 2022; 298:102548. [PMID: 36181794 PMCID: PMC9626948 DOI: 10.1016/j.jbc.2022.102548] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 09/22/2022] [Accepted: 09/23/2022] [Indexed: 12/02/2022] Open
Abstract
The evolutionarily conserved bacterial proteins MnmE and MnmG collectively install a carboxymethylaminomethyl (cmnm) group at the fifth position of wobble uridines of several tRNA species. While the reaction catalyzed by MnmEG is one of the central steps in the biosynthesis of the methylaminomethyl (mnm) posttranscriptional tRNA modification, details of the reaction remain elusive. Glycine is known to be the source of the carboxy methylamino moiety of cmnm, and a tetrahydrofolate (THF) analog is thought to supply the one carbon that is appended to the fifth position of U. However, the nature of the folate analog remains unknown. This article reports the in vitro biochemical reconstitution of the MnmEG reaction. Using isotopically labeled methyl and methylene THF analogs, we demonstrate that methylene THF is the true substrate. We also show that reduced FAD is required for the reaction and that DTT can replace the NADH in its role as a reductant. We discuss the implications of these methylene-THF and reductant requirements on the mechanism of this key tRNA modification catalyzed by MnmEG.
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Affiliation(s)
- Praneeth Bommisetti
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
| | - Anthony Young
- Soliome Inc, 479 Jessie Street, San Francisco, CA 94103, United States
| | - Vahe Bandarian
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States.
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7
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Kwon CW, Chung B, Yoo SH, Chang PS. Heterologous expression of a papain-like protease inhibitor (SnuCalCpI17) in the E. coli and its mode of inhibition. Appl Microbiol Biotechnol 2022; 106:4563-4574. [PMID: 35748913 DOI: 10.1007/s00253-022-12032-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Revised: 06/10/2022] [Accepted: 06/14/2022] [Indexed: 11/30/2022]
Abstract
The effect of the Escherichia coli (E. coli) Rosetta (DE3) system on the expression of recombinant papain-like cysteine protease inhibitors (SnuCalCpIs) was evaluated, and the inhibition mode of the expressed inhibitor was determined. SnuCalCpI08 and SnuCalCpI17, which previously had not been expressed in the E. coli BL21 (DE3) system due to rare codons of more than 10%, were successfully expressed in E. coli Rosetta (DE3) since the strain provides tRNAs for six rare codons. Initially, both inhibitors were expressed as inclusion bodies; however, the water solubility of SnuCalCpI17 could be improved by lowering the incubation temperature, reducing the IPTG concentration, and increasing the induction time. In contrast, the other inhibitor could not be solubilized in water. To validate whether the inhibitor was expressed with correct protein folding, a papain inhibition assay was performed with SnuCalCpI17. SnuCalCpI17 showed a half-maximal inhibitory concentration (IC50) of 105.671 ± 9.857 µg/mL and a slow-binding inhibition mode against papain at pH 7.0 with a Kiapp of 75.80 μg/mL. The slow-binding inhibitor has a slow dissociation from the inhibitor-target complex, resulting in a long residence time in vivo, and thus can effectively inhibit the target at doses far below the IC50 of the inhibitor. KEY POINTS: • Propeptide inhibitor (SnuCalCpI17) containing rare codons was expressed in E. coli Rosetta (DE3). • The slow-binding inhibition was shown by plotting the apparent first-order rate constant (kobs). • Protein-protein interaction between SnuCalCpIs and papain was verified by docking simulation.
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Affiliation(s)
- Chang Woo Kwon
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Bokyong Chung
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, Republic of Korea
| | - Sang-Ho Yoo
- Department of Food Science & Biotechnology, and Carbohydrate Bioproduct Research Center, Sejong University, Seoul, 05006, Republic of Korea
| | - Pahn-Shick Chang
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea. .,Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, Republic of Korea. .,Center for Food and Bioconvergence, Seoul National University, Seoul, 08826, Republic of Korea. .,Center for Agricultural Microorganism and Enzyme, Seoul National University, Seoul, 08826, Republic of Korea.
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8
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Manavski N, Vicente A, Chi W, Meurer J. The Chloroplast Epitranscriptome: Factors, Sites, Regulation, and Detection Methods. Genes (Basel) 2021; 12:genes12081121. [PMID: 34440296 PMCID: PMC8394491 DOI: 10.3390/genes12081121] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 07/20/2021] [Accepted: 07/22/2021] [Indexed: 12/24/2022] Open
Abstract
Modifications in nucleic acids are present in all three domains of life. More than 170 distinct chemical modifications have been reported in cellular RNAs to date. Collectively termed as epitranscriptome, these RNA modifications are often dynamic and involve distinct regulatory proteins that install, remove, and interpret these marks in a site-specific manner. Covalent nucleotide modifications-such as methylations at diverse positions in the bases, polyuridylation, and pseudouridylation and many others impact various events in the lifecycle of an RNA such as folding, localization, processing, stability, ribosome assembly, and translational processes and are thus crucial regulators of the RNA metabolism. In plants, the nuclear/cytoplasmic epitranscriptome plays important roles in a wide range of biological processes, such as organ development, viral infection, and physiological means. Notably, recent transcriptome-wide analyses have also revealed novel dynamic modifications not only in plant nuclear/cytoplasmic RNAs related to photosynthesis but especially in chloroplast mRNAs, suggesting important and hitherto undefined regulatory steps in plastid functions and gene expression. Here we report on the latest findings of known plastid RNA modifications and highlight their relevance for the post-transcriptional regulation of chloroplast gene expression and their role in controlling plant development, stress reactions, and acclimation processes.
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Affiliation(s)
- Nikolay Manavski
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-University Munich, Großhaderner Street 2-4, 82152 Planegg-Martinsried, Germany; (N.M.); (A.V.)
| | - Alexandre Vicente
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-University Munich, Großhaderner Street 2-4, 82152 Planegg-Martinsried, Germany; (N.M.); (A.V.)
| | - Wei Chi
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China;
| | - Jörg Meurer
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-University Munich, Großhaderner Street 2-4, 82152 Planegg-Martinsried, Germany; (N.M.); (A.V.)
- Correspondence: ; Tel.: +49-89-218074556
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9
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Antoine L, Bahena-Ceron R, Devi Bunwaree H, Gobry M, Loegler V, Romby P, Marzi S. RNA Modifications in Pathogenic Bacteria: Impact on Host Adaptation and Virulence. Genes (Basel) 2021; 12:1125. [PMID: 34440299 PMCID: PMC8394870 DOI: 10.3390/genes12081125] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 07/16/2021] [Accepted: 07/19/2021] [Indexed: 12/19/2022] Open
Abstract
RNA modifications are involved in numerous biological processes and are present in all RNA classes. These modifications can be constitutive or modulated in response to adaptive processes. RNA modifications play multiple functions since they can impact RNA base-pairings, recognition by proteins, decoding, as well as RNA structure and stability. However, their roles in stress, environmental adaptation and during infections caused by pathogenic bacteria have just started to be appreciated. With the development of modern technologies in mass spectrometry and deep sequencing, recent examples of modifications regulating host-pathogen interactions have been demonstrated. They show how RNA modifications can regulate immune responses, antibiotic resistance, expression of virulence genes, and bacterial persistence. Here, we illustrate some of these findings, and highlight the strategies used to characterize RNA modifications, and their potential for new therapeutic applications.
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Affiliation(s)
| | | | | | | | | | | | - Stefano Marzi
- Université de Strasbourg, CNRS, Architecture et Réactivité de l’ARN, UPR 9002, F-67000 Strasbourg, France; (L.A.); (R.B.-C.); (H.D.B.); (M.G.); (V.L.); (P.R.)
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10
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Lindarto WW, Wasito EB, Debora K. Effect of Glucose Induction on Biofilm Density in Clinical Isolate Acinetobacter baumannii Patients in Intensive Care Unit of Dr. Soetomo Hospital, Surabaya. FOLIA MEDICA INDONESIANA 2020. [DOI: 10.20473/fmi.v56i2.21230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
This study aimed to analyze the effect of glucose induction on the clinical isolate biofilm density of Acinetobacter baumannii. Thirteen clinical isolates of A. baumannii non biofilm forming were collected from non-DM patients who were treated at the ICU of Dr. Soetomo Hospital, Surabaya, was treated with the addition of 0.08% glucose, 0.15% glucose, 0.2% glucose, and 0.4% glucose in TSB growth media, followed by biofilm density examination with Tissue Culture Plate Method (TCPM) using 96 wells flatbottomed polyesterene tissue culture plate and read by autoreader ELISA with a wavelength of 630 nm (OD630). Biofilm density obtained was analyzed using ANOVA statistical analysis. The results of OD630 showed that the biofilm density increased significantly at the addition of 0.2% and 0.4% glucose. There was a significant increase in biofilm density at the addition of 0.2% and 0.4% glucose so that the management of blood sugar levels in ICU patients was needed before and when medical devices were installed.
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11
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Liu H, Ren D, Jiang L, Li X, Yao Y, Mi L, Chen W, Mo A, Jiang N, Yang J, Chen P, Ma H, Luo X, Lu P. A Natural Variation in PLEIOTROPIC DEVELOPMENTAL DEFECTS Uncovers a Crucial Role for Chloroplast tRNA Modification in Translation and Plant Development. THE PLANT CELL 2020; 32:2345-2366. [PMID: 32327539 PMCID: PMC7346568 DOI: 10.1105/tpc.19.00660] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 03/30/2020] [Accepted: 04/15/2020] [Indexed: 05/28/2023]
Abstract
The modification of tRNA is important for accurate, efficient protein translation. A number of tRNA-modifying enzymes were found to influence various developmental processes in distinct organisms. However, few genetic or molecular studies have focused on genes encoding tRNA-modifying enzymes in green plant organelles. Here, we discovered that PDD OL , a natural variation allele of PLEIOTROPIC DEVELOPMENTAL DEFECTS (PDD), leads to pleiotropic developmental defects in a near-isogenic line (NIL) generated by introgressing the wild rice Oryza longistaminata into the rice (Oryza sativa) cv 187R. Map-based cloning revealed that PDD encodes an evolutionarily conserved tRNA-modifying GTPase belonging to the tRNA modification E family. The function of PDD was further confirmed by genetic complementation experiments and mutant analysis. PDD mRNA is primarily expressed in leaves, and PDD is localized to chloroplasts. Biochemical analyses indicated that PDD187R forms homodimers and has strong GTPase activity, whereas PDDOL fails to form homodimers and has weak GTPase activity. Liquid chromatography-coupled tandem quadrupole mass spectrometry revealed that PDD is associated with the 5-methylaminomethyl-2-thiouridine modification of chloroplast tRNA. Furthermore, compared to 187R, NIL-PDD OL has severely reduced levels of proteins involved in photosynthesis and ribosome biogenesis but increased levels of plastid-encoded RNA polymerase subunits. Finally, we demonstrate that the defect due to PDD OL alters chloroplast gene expression, thereby affecting communication between the chloroplast and the nucleus.
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Affiliation(s)
- Hui Liu
- School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Ding Ren
- School of Life Sciences, Fudan University, Shanghai 200433, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Ling Jiang
- School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Xiaojing Li
- School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Yuan Yao
- School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Limin Mi
- School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Wanli Chen
- School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Aowei Mo
- School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Ning Jiang
- School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Jinshui Yang
- School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Peng Chen
- Biomass and Bioenergy Research Centre, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hong Ma
- Department of Biology, Eberly College of Science, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802
| | - Xiaojin Luo
- School of Life Sciences, Fudan University, Shanghai 200433, China
- MOE Engineering Research Center of Gene Technology, Fudan University, Shanghai 200433, China
| | - Pingli Lu
- School of Life Sciences, Fudan University, Shanghai 200433, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
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12
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Angelova MT, Dimitrova DG, Da Silva B, Marchand V, Jacquier C, Achour C, Brazane M, Goyenvalle C, Bourguignon-Igel V, Shehzada S, Khouider S, Lence T, Guerineau V, Roignant JY, Antoniewski C, Teysset L, Bregeon D, Motorin Y, Schaefer MR, Carré C. tRNA 2'-O-methylation by a duo of TRM7/FTSJ1 proteins modulates small RNA silencing in Drosophila. Nucleic Acids Res 2020; 48:2050-2072. [PMID: 31943105 PMCID: PMC7038984 DOI: 10.1093/nar/gkaa002] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 12/30/2019] [Accepted: 01/01/2020] [Indexed: 12/14/2022] Open
Abstract
2′-O-Methylation (Nm) represents one of the most common RNA modifications. Nm affects RNA structure and function with crucial roles in various RNA-mediated processes ranging from RNA silencing, translation, self versus non-self recognition to viral defense mechanisms. Here, we identify two Nm methyltransferases (Nm-MTases) in Drosophila melanogaster (CG7009 and CG5220) as functional orthologs of yeast TRM7 and human FTSJ1. Genetic knockout studies together with MALDI-TOF mass spectrometry and RiboMethSeq mapping revealed that CG7009 is responsible for methylating the wobble position in tRNAPhe, tRNATrp and tRNALeu, while CG5220 methylates position C32 in the same tRNAs and also targets additional tRNAs. CG7009 or CG5220 mutant animals were viable and fertile but exhibited various phenotypes such as lifespan reduction, small RNA pathways dysfunction and increased sensitivity to RNA virus infections. Our results provide the first detailed characterization of two TRM7 family members in Drosophila and uncover a molecular link between enzymes catalyzing Nm at specific tRNAs and small RNA-induced gene silencing pathways.
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Affiliation(s)
- Margarita T Angelova
- Transgenerational Epigenetics & small RNA Biology, Sorbonne Université, Centre National de la Recherche Scientifique, Laboratoire de Biologie du Développement - Institut de Biologie Paris Seine, 9 Quai Saint Bernard, 75005 Paris, France
| | - Dilyana G Dimitrova
- Transgenerational Epigenetics & small RNA Biology, Sorbonne Université, Centre National de la Recherche Scientifique, Laboratoire de Biologie du Développement - Institut de Biologie Paris Seine, 9 Quai Saint Bernard, 75005 Paris, France
| | - Bruno Da Silva
- Transgenerational Epigenetics & small RNA Biology, Sorbonne Université, Centre National de la Recherche Scientifique, Laboratoire de Biologie du Développement - Institut de Biologie Paris Seine, 9 Quai Saint Bernard, 75005 Paris, France
| | - Virginie Marchand
- Next-Generation Sequencing Core Facility, UMS2008 IBSLor CNRS-Université de Lorraine-INSERM, BioPôle, 9 avenue de la Forêt de Haye, 54505 Vandoeuvre-les-Nancy, France
| | - Caroline Jacquier
- Transgenerational Epigenetics & small RNA Biology, Sorbonne Université, Centre National de la Recherche Scientifique, Laboratoire de Biologie du Développement - Institut de Biologie Paris Seine, 9 Quai Saint Bernard, 75005 Paris, France
| | - Cyrinne Achour
- Transgenerational Epigenetics & small RNA Biology, Sorbonne Université, Centre National de la Recherche Scientifique, Laboratoire de Biologie du Développement - Institut de Biologie Paris Seine, 9 Quai Saint Bernard, 75005 Paris, France
| | - Mira Brazane
- Transgenerational Epigenetics & small RNA Biology, Sorbonne Université, Centre National de la Recherche Scientifique, Laboratoire de Biologie du Développement - Institut de Biologie Paris Seine, 9 Quai Saint Bernard, 75005 Paris, France
| | - Catherine Goyenvalle
- Eucaryiotic Translation, Sorbonne Université, CNRS, Institut de Biologie Paris Seine, Biological Adaptation and Ageing, Institut de Biologie Paris Seine, 9 Quai Saint bernard, 75005 Paris, France
| | - Valérie Bourguignon-Igel
- Next-Generation Sequencing Core Facility, UMS2008 IBSLor CNRS-Université de Lorraine-INSERM, BioPôle, 9 avenue de la Forêt de Haye, 54505 Vandoeuvre-les-Nancy, France.,Ingénierie Moléculaire et Physiopathologie Articulaire, UMR7365, CNRS - Université de Lorraine, 9 avenue de la Forêt de Haye, 54505 Vandoeuvre-les-Nancy, France
| | - Salman Shehzada
- Transgenerational Epigenetics & small RNA Biology, Sorbonne Université, Centre National de la Recherche Scientifique, Laboratoire de Biologie du Développement - Institut de Biologie Paris Seine, 9 Quai Saint Bernard, 75005 Paris, France
| | - Souraya Khouider
- Transgenerational Epigenetics & small RNA Biology, Sorbonne Université, Centre National de la Recherche Scientifique, Laboratoire de Biologie du Développement - Institut de Biologie Paris Seine, 9 Quai Saint Bernard, 75005 Paris, France
| | - Tina Lence
- Institute of Molecular Biology, Ackermannweg 4, 55128, Mainz, Germany
| | - Vincent Guerineau
- Institut de Chimie de Substances Naturelles, Centre de Recherche de Gif CNRS, 1 avenue de la Terrasse, 91198 Gif-sur-Yvette, France
| | - Jean-Yves Roignant
- Institute of Molecular Biology, Ackermannweg 4, 55128, Mainz, Germany.,Center for Integrative Genomics, Génopode Building, Faculty of Biology and Medicine, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Christophe Antoniewski
- ARTbio Bioinformatics Analysis Facility, Sorbonne Université, CNRS, Institut de Biologie Paris Seine, 9 Quai Saint Bernard, 75005 Paris, France
| | - Laure Teysset
- Transgenerational Epigenetics & small RNA Biology, Sorbonne Université, Centre National de la Recherche Scientifique, Laboratoire de Biologie du Développement - Institut de Biologie Paris Seine, 9 Quai Saint Bernard, 75005 Paris, France
| | - Damien Bregeon
- Eucaryiotic Translation, Sorbonne Université, CNRS, Institut de Biologie Paris Seine, Biological Adaptation and Ageing, Institut de Biologie Paris Seine, 9 Quai Saint bernard, 75005 Paris, France
| | - Yuri Motorin
- Ingénierie Moléculaire et Physiopathologie Articulaire, UMR7365, CNRS - Université de Lorraine, 9 avenue de la Forêt de Haye, 54505 Vandoeuvre-les-Nancy, France
| | - Matthias R Schaefer
- Division of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, Schwarzspanierstrasse 17, A-1090 Vienna, Austria
| | - Clément Carré
- Transgenerational Epigenetics & small RNA Biology, Sorbonne Université, Centre National de la Recherche Scientifique, Laboratoire de Biologie du Développement - Institut de Biologie Paris Seine, 9 Quai Saint Bernard, 75005 Paris, France
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13
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Erfan AM, Marouf S. Cinnamon oil downregulates virulence genes of poultry respiratory bacterial agents and revealed significant bacterial inhibition: An in vitro perspective. Vet World 2019; 12:1707-1715. [PMID: 32009749 PMCID: PMC6925043 DOI: 10.14202/vetworld.2019.1707-1715] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Accepted: 09/30/2019] [Indexed: 11/16/2022] Open
Abstract
Background and Aim: Respiratory bacterial agents represent one of the most harmful factors that ordinarily threaten the poultry industry and usually lead to great economic losses. Meanwhile, there is a global demand to avoid the highly emerging antibiotic resistance and antibiotic residues in edible meat. Whereas, the use of alternatives became of great priority, especially for those substances extracted from natural plant origin. The study aimed to evaluate the antibacterial effect of cinnamon oil as a herbal extract on different respiratory bacterial agents. Materials and Methods: One hundred and fifty biological samples were collected through targeted surveillance for respiratory diseased poultry farms representing three governorates, from which bacterial isolation and identification, DNA sequencing of representative strains were performed. Furtherly, phenotypic and genotypic evaluation of the antibacterial effect of cinnamon oil was performed by minimum inhibitory concentration, agar disk diffusion, and virulence genes expression real-time polymerase chain reaction. Results: Cinnamon oil gave rise to acceptable degrees of virulence genes downregulation of 0.15, 0.19, 0.37, 0.41, 0.77, and 0.85 for Staphylococcus aureus sed gene, Escherichia coli stx1 gene, Avibacterium paragallinarum HPG-2 gene, Pasteurella multocida ptfA gene, Mycoplasma gallisepticum Mgc2 gene, and Ornithobacterium rhinotracheale adk gene, respectively. Phenotypically, using agar disk diffusion assay and broth microdilution susceptibility, cinnamon oil showed also tolerable results as it stopped the growth of S. aureus, E. coli, P. multocida, and A. paragallinarum with varying zones of inhibition. Conclusion: The encountered results declared the successful in vitro effect of cinnamon oil that recommends its application for living birds for future use as a safe antibacterial in the poultry industry.
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Affiliation(s)
- Ahmed Mohammed Erfan
- National Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Dokki, Giza, 12618, Egypt
| | - Sherif Marouf
- Department of Microbiology, Faculty of Veterinary Medicine, Cairo University, Giza, 12211, Egypt
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14
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Antoine L, Wolff P, Westhof E, Romby P, Marzi S. Mapping post-transcriptional modifications in Staphylococcus aureus tRNAs by nanoLC/MSMS. Biochimie 2019; 164:60-69. [PMID: 31295507 DOI: 10.1016/j.biochi.2019.07.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 07/03/2019] [Indexed: 02/06/2023]
Abstract
RNA modifications are involved in numerous biological processes. These modifications are constitutive or modulated in response to adaptive processes and can impact RNA base-pairing formation, protein recognition, RNA structure and stability. tRNAs are the most abundantly modified RNA molecules. Analysis of the roles of their modifications in response to stress, environmental changes, and infections caused by pathogens, has fueled new research areas. Nevertheless, the detection of modified nucleotides in RNAs is still a challenging task. We present here a reliable method to identify and localize tRNA modifications, which was applied to the human pathogenic bacteria, Staphyloccocus aureus. The method is based on a separation of tRNA species on a two-dimensional polyacrylamide gel electrophoresis followed by nano liquid chromatography-mass spectrometry. We provided a list of modifications mapped on 25 out of the 40 tRNA species (one isoacceptor for each amino acid). This method can be easily used to monitor the dynamics of tRNA modifications in S. aureus in response to stress adaptation and during infection of the host, a relatively unexplored field.
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Affiliation(s)
- Laura Antoine
- Université de Strasbourg, CNRS, Architecture et Réactivité de L'ARN, UPR 9002, F-67000, Strasbourg, France
| | - Philippe Wolff
- Université de Strasbourg, CNRS, Architecture et Réactivité de L'ARN, UPR 9002, F-67000, Strasbourg, France; Plateforme Protéomique Strasbourg Esplanade, CNRS, FR1589, F-67000, Strasbourg, France
| | - Eric Westhof
- Université de Strasbourg, CNRS, Architecture et Réactivité de L'ARN, UPR 9002, F-67000, Strasbourg, France
| | - Pascale Romby
- Université de Strasbourg, CNRS, Architecture et Réactivité de L'ARN, UPR 9002, F-67000, Strasbourg, France
| | - Stefano Marzi
- Université de Strasbourg, CNRS, Architecture et Réactivité de L'ARN, UPR 9002, F-67000, Strasbourg, France.
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15
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Swarge BN, Roseboom W, Zheng L, Abhyankar WR, Brul S, de Koster CG, de Koning LJ. "One-Pot" Sample Processing Method for Proteome-Wide Analysis of Microbial Cells and Spores. Proteomics Clin Appl 2018; 12:e1700169. [PMID: 29484825 PMCID: PMC6174930 DOI: 10.1002/prca.201700169] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 01/22/2018] [Indexed: 11/15/2022]
Abstract
PURPOSE Bacterial endospores, the transmissible forms of pathogenic bacilli and clostridia, are heterogeneous multilayered structures composed of proteins. These proteins protect the spores against a variety of stresses, thus helping spore survival, and assist in germination, by interacting with the environment to form vegetative cells. Owing to the complexity, insolubility, and dynamic nature of spore proteins, it has been difficult to obtain their comprehensive protein profiles. EXPERIMENTAL DESIGN The intact spores of Bacillus subtilis, Bacillus cereus, and Peptoclostridium difficile and their vegetative counterparts were disrupted by bead beating in 6 m urea under reductive conditions. The heterogeneous mixture was then double digested with LysC and trypsin. Next, the peptide mixture was pre-fractionated with zwitterionic hydrophilic interaction liquid chromatography (ZIC-HILIC) followed by reverse-phase LC-FT-MS analysis of the fractions. RESULTS "One-pot" method is a simple, robust method that yields identification of >1000 proteins with high confidence, across all spore layers from B. subtilis, B. cereus, and P. difficile. CONCLUSIONS AND MEDICAL RELEVANCE This method can be employed for proteome-wide analysis of non-spore-forming as well as spore-forming pathogens. Analysis of spore protein profile will help to understand the sporulation and germination processes and to distinguish immunogenic protein markers.
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Affiliation(s)
- Bhagyashree Nandakishor Swarge
- Department of Mass Spectrometry of Bio macromolecules, University of Amsterdam, Amsterdam, The Netherlands
- Department of Molecular Biology and Microbial Food Safety, Swammerdam Institutes of Life Sciences, University of Amsterdam, The Netherlands
| | - Winfried Roseboom
- Department of Mass Spectrometry of Bio macromolecules, University of Amsterdam, Amsterdam, The Netherlands
| | - Linli Zheng
- Department of Mass Spectrometry of Bio macromolecules, University of Amsterdam, Amsterdam, The Netherlands
- Department of Molecular Biology and Microbial Food Safety, Swammerdam Institutes of Life Sciences, University of Amsterdam, The Netherlands
| | - Wishwas R Abhyankar
- Department of Mass Spectrometry of Bio macromolecules, University of Amsterdam, Amsterdam, The Netherlands
- Department of Molecular Biology and Microbial Food Safety, Swammerdam Institutes of Life Sciences, University of Amsterdam, The Netherlands
| | - Stanley Brul
- Department of Molecular Biology and Microbial Food Safety, Swammerdam Institutes of Life Sciences, University of Amsterdam, The Netherlands
| | - Chris G de Koster
- Department of Mass Spectrometry of Bio macromolecules, University of Amsterdam, Amsterdam, The Netherlands
| | - Leo J de Koning
- Department of Mass Spectrometry of Bio macromolecules, University of Amsterdam, Amsterdam, The Netherlands
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16
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Thailandamide, a Fatty Acid Synthesis Antibiotic That Is Coexpressed with a Resistant Target Gene. Antimicrob Agents Chemother 2018; 62:AAC.00463-18. [PMID: 29914944 DOI: 10.1128/aac.00463-18] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 06/09/2018] [Indexed: 12/25/2022] Open
Abstract
Microbes encode many uncharacterized gene clusters that may produce antibiotics and other bioactive small molecules. Methods for activating these genes are needed to explore their biosynthetic potential. A transposon containing an inducible promoter was randomly inserted into the genome of the soil bacterium Burkholderia thailandensis to induce antibiotic expression. This screen identified the polyketide/nonribosomal peptide thailandamide as an antibiotic and discovered its regulator, AtsR. Mutants of Salmonella resistant to thailandamide had mutations in the accA gene for acetyl coenzyme A (acetyl-CoA) carboxylase, which is one of the first enzymes in the fatty acid synthesis pathway. A second copy of accA in the thailandamide synthesis gene cluster keeps B. thailandensis resistant to its own antibiotic. These genetic techniques will likely be powerful tools for discovering other unusual antibiotics.
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17
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Defects in the mitochondrial-tRNA modification enzymes MTO1 and GTPBP3 promote different metabolic reprogramming through a HIF-PPARγ-UCP2-AMPK axis. Sci Rep 2018; 8:1163. [PMID: 29348686 PMCID: PMC5773609 DOI: 10.1038/s41598-018-19587-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 01/04/2018] [Indexed: 12/12/2022] Open
Abstract
Human proteins MTO1 and GTPBP3 are thought to jointly catalyze the modification of the wobble uridine in mitochondrial tRNAs. Defects in each protein cause infantile hypertrophic cardiomyopathy with lactic acidosis. However, the underlying mechanisms are mostly unknown. Using fibroblasts from an MTO1 patient and MTO1 silenced cells, we found that the MTO1 deficiency is associated with a metabolic reprogramming mediated by inactivation of AMPK, down regulation of the uncoupling protein 2 (UCP2) and transcription factor PPARγ, and activation of the hypoxia inducible factor 1 (HIF-1). As a result, glycolysis and oxidative phosphorylation are uncoupled, while fatty acid metabolism is altered, leading to accumulation of lipid droplets in MTO1 fibroblasts. Unexpectedly, this response is different from that triggered by the GTPBP3 defect, as GTPBP3-depleted cells exhibit AMPK activation, increased levels of UCP2 and PPARγ, and inactivation of HIF-1. In addition, fatty acid oxidation and respiration are stimulated in these cells. Therefore, the HIF-PPARγ-UCP2-AMPK axis is operating differently in MTO1- and GTPBP3-defective cells, which strongly suggests that one of these proteins has an additional role, besides mitochondrial-tRNA modification. This work provides new and useful information on the molecular basis of the MTO1 and GTPBP3 defects and on putative targets for therapeutic intervention.
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18
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19
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Mutations in the Caenorhabditis elegans orthologs of human genes required for mitochondrial tRNA modification cause similar electron transport chain defects but different nuclear responses. PLoS Genet 2017; 13:e1006921. [PMID: 28732077 PMCID: PMC5544249 DOI: 10.1371/journal.pgen.1006921] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 08/04/2017] [Accepted: 07/13/2017] [Indexed: 11/19/2022] Open
Abstract
Several oxidative phosphorylation (OXPHOS) diseases are caused by defects in the post-transcriptional modification of mitochondrial tRNAs (mt-tRNAs). Mutations in MTO1 or GTPBP3 impair the modification of the wobble uridine at position 5 of the pyrimidine ring and cause heart failure. Mutations in TRMU affect modification at position 2 and cause liver disease. Presently, the molecular basis of the diseases and why mutations in the different genes lead to such different clinical symptoms is poorly understood. Here we use Caenorhabditis elegans as a model organism to investigate how defects in the TRMU, GTPBP3 and MTO1 orthologues (designated as mttu-1, mtcu-1, and mtcu-2, respectively) exert their effects. We found that whereas the inactivation of each C. elegans gene is associated with a mild OXPHOS dysfunction, mutations in mtcu-1 or mtcu-2 cause changes in the expression of metabolic and mitochondrial stress response genes that are quite different from those caused by mttu-1 mutations. Our data suggest that retrograde signaling promotes defect-specific metabolic reprogramming, which is able to rescue the OXPHOS dysfunction in the single mutants by stimulating the oxidative tricarboxylic acid cycle flux through complex II. This adaptive response, however, appears to be associated with a biological cost since the single mutant worms exhibit thermosensitivity and decreased fertility and, in the case of mttu-1, longer reproductive cycle. Notably, mttu-1 worms also exhibit increased lifespan. We further show that mtcu-1; mttu-1 and mtcu-2; mttu-1 double mutants display severe growth defects and sterility. The animal models presented here support the idea that the pathological states in humans may initially develop not as a direct consequence of a bioenergetic defect, but from the cell’s maladaptive response to the hypomodification status of mt-tRNAs. Our work highlights the important association of the defect-specific metabolic rewiring with the pathological phenotype, which must be taken into consideration in exploring specific therapeutic interventions. Post-transcriptional modification of tRNAs is a universal process, thought to be essential for optimizing the functions of tRNAs. In humans, defects in the modification at position 2 (performed by protein TRMU) and 5 (carried out by proteins GTPBP3 and MTO1) of the uridine located at the wobble position of mitochondrial tRNAs (mt-tRNAs) cause oxidative phosphorylation (OXPHOS) dysfunction, and lead to liver and heart failure, respectively. However, the underlying mechanisms leading to pathogenesis are not well-known, and hence there is no molecular explanation for the different clinical phenotypes. We use Caenorhabditis elegans to compare in the same animal model and genetic background the effects of inactivating the TRMU, GTPBP3 and MTO1 orthologues on the phenotype and gene expression pattern of nuclear and mitochondrial DNA. Our data show that C. elegans responds to mt-tRNA hypomodification by changing in a defect-specific manner the expression of nuclear and mitochondrial genes, which leads, in all single mutants, to a rescue of the OXPHOS dysfunction that is associated with a biological cost. Our work suggests that pathology may develop as a consequence of the cell’s maladaptive response to the hypomodification status of mt-tRNAs.
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20
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Biosynthesis of Sulfur-Containing tRNA Modifications: A Comparison of Bacterial, Archaeal, and Eukaryotic Pathways. Biomolecules 2017; 7:biom7010027. [PMID: 28287455 PMCID: PMC5372739 DOI: 10.3390/biom7010027] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 03/03/2017] [Accepted: 03/06/2017] [Indexed: 01/12/2023] Open
Abstract
Post-translational tRNA modifications have very broad diversity and are present in all domains of life. They are important for proper tRNA functions. In this review, we emphasize the recent advances on the biosynthesis of sulfur-containing tRNA nucleosides including the 2-thiouridine (s2U) derivatives, 4-thiouridine (s4U), 2-thiocytidine (s2C), and 2-methylthioadenosine (ms2A). Their biosynthetic pathways have two major types depending on the requirement of iron–sulfur (Fe–S) clusters. In all cases, the first step in bacteria and eukaryotes is to activate the sulfur atom of free l-cysteine by cysteine desulfurases, generating a persulfide (R-S-SH) group. In some archaea, a cysteine desulfurase is missing. The following steps of the bacterial s2U and s4U formation are Fe–S cluster independent, and the activated sulfur is transferred by persulfide-carrier proteins. By contrast, the biosynthesis of bacterial s2C and ms2A require Fe–S cluster dependent enzymes. A recent study shows that the archaeal s4U synthetase (ThiI) and the eukaryotic cytosolic 2-thiouridine synthetase (Ncs6) are Fe–S enzymes; this expands the role of Fe–S enzymes in tRNA thiolation to the Archaea and Eukarya domains. The detailed reaction mechanisms of Fe–S cluster depend s2U and s4U formation await further investigations.
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21
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Lee C, Kim J, Kwon M, Lee K, Min H, Kim SH, Kim D, Lee N, Kim J, Kim D, Ko C, Park C. Screening for Escherichia coli K-12 genes conferring glyoxal resistance or sensitivity by transposon insertions. FEMS Microbiol Lett 2016; 363:fnw199. [PMID: 27535647 DOI: 10.1093/femsle/fnw199] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/12/2016] [Indexed: 12/14/2022] Open
Abstract
Glyoxal (GO) belongs to the reactive electrophilic species generated in vivo in all organisms. In order to identify targets of GO and their response mechanisms, we attempted to screen for GO-sensitive mutants by random insertions of TnphoA-132. The genes responsible for GO susceptibility were functionally classified as the following: (i) tRNA modification; trmE, gidA and truA, (ii) DNA repair; recA and recC, (iii) toxin-antitoxin; mqsA and (iv) redox metabolism; yqhD and caiC In addition, an insertion in the crp gene, encoding the cAMP responsive transcription factor, exhibits a GO-resistant phenotype, which is consistent with the phenotype of adenylate cyclase (cya) mutant showing GO resistance. This suggests that global regulation involving cAMP is operated in a stress response to GO. To further characterize the CRP-regulated genes directly associated with GO resistance, we created double mutants deficient in both crp and one of the candidate genes including yqhD, gloA and sodB The results indicate that these genes are negatively regulated by CRP as confirmed by real-time RT-PCR. We propose that tRNA as well as DNA are the targets of GO and that toxin/antitoxin, antioxidant and cAMP are involved in cellular response to GO.
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Affiliation(s)
- Changhan Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Yuseong-gu, Daejeon 305-701, Republic of Korea
| | - Jihong Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Yuseong-gu, Daejeon 305-701, Republic of Korea
| | - Minsuk Kwon
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Yuseong-gu, Daejeon 305-701, Republic of Korea
| | - Kihyun Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Yuseong-gu, Daejeon 305-701, Republic of Korea
| | - Haeyoung Min
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Yuseong-gu, Daejeon 305-701, Republic of Korea
| | - Seong Hun Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Yuseong-gu, Daejeon 305-701, Republic of Korea
| | - Dongkyu Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Yuseong-gu, Daejeon 305-701, Republic of Korea
| | - Nayoung Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Yuseong-gu, Daejeon 305-701, Republic of Korea
| | - Jiyeun Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Yuseong-gu, Daejeon 305-701, Republic of Korea
| | - Doyun Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Yuseong-gu, Daejeon 305-701, Republic of Korea
| | - Changmin Ko
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Yuseong-gu, Daejeon 305-701, Republic of Korea
| | - Chankyu Park
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Yuseong-gu, Daejeon 305-701, Republic of Korea
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Satapathy SS, Powdel BR, Buragohain AK, Ray SK. Discrepancy among the synonymous codons with respect to their selection as optimal codon in bacteria. DNA Res 2016; 23:441-449. [PMID: 27426467 PMCID: PMC5066170 DOI: 10.1093/dnares/dsw027] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 05/19/2016] [Indexed: 01/05/2023] Open
Abstract
The different triplets encoding the same amino acid, termed as synonymous codons, are not equally abundant in a genome. Factors such as G + C% and tRNA are known to influence their abundance in a genome. However, the order of the nucleotide in each codon per se might also be another factor impacting on its abundance values. Of the synonymous codons for specific amino acids, some are preferentially used in the high expression genes that are referred to as the 'optimal codons' (OCs). In this study, we compared OCs of the 18 amino acids in 221 species of bacteria. It is observed that there is amino acid specific influence for the selection of OCs. There is also influence of phylogeny in the choice of OCs for some amino acids such as Glu, Gln, Lys and Leu. The phenomenon of codon bias is also supported by the comparative studies of the abundance values of the synonymous codons with same G + C. It is likely that the order of the nucleotides in the triplet codon is also perhaps involved in the phenomenon of codon usage bias in organisms.
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Affiliation(s)
| | - Bhesh Raj Powdel
- Department of Statistics, Darrang College, Tezpur 784001, Assam, India
| | - Alak Kumar Buragohain
- Department of Molecular Biology and Biotechnology, Tezpur University, Napaam, Tezpur 784028, Assam, India.,Office of the Vice-Chancellor, Dibrugarh University, Dibrugarh 786004, Assam, India
| | - Suvendra Kumar Ray
- Department of Molecular Biology and Biotechnology, Tezpur University, Napaam, Tezpur 784028, Assam, India
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Chen D, Li F, Yang Q, Tian M, Zhang Z, Zhang Q, Chen Y, Guan MX. The defective expression of gtpbp3 related to tRNA modification alters the mitochondrial function and development of zebrafish. Int J Biochem Cell Biol 2016; 77:1-9. [PMID: 27184967 DOI: 10.1016/j.biocel.2016.05.012] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Revised: 05/02/2016] [Accepted: 05/12/2016] [Indexed: 01/13/2023]
Abstract
Human mitochondrial DNA (mtDNA) mutations have been associated with a wide spectrum of clinical abnormalities. However, nuclear modifier gene(s) modulate the phenotypic expression of pathogenic mtDNA mutations. In our previous investigation, we identified the human GTPBP3 related to mitochondrial tRNA modification, acting as a modifier to influence of deafness-associated mtDNA mutation. Mutations in GTPBP3 have been found to be associated with other human diseases. However, the pathophysiology of GTPBP3-associated disorders is still not fully understood. Here, we reported the generation and characterization of Gtpbp3 depletion zebrafish model using antisense morpholinos. Zebrafish gtpbp3 has three isoforms localized at mitochondria. Zebrafish gtpbp3 is expressed at various embryonic stages and in multiple tissues. In particular, the gtpbp3 was expressed more abundantly in adult zebrafish ovary and testis. The expression of zebrafish gtpbp3 can functionally restore the growth defects caused by the mss1/gtpbp3 mutation in yeast. A marked decrease of mitochondrial ATP generation accompanied by increased levels of apoptosis and reactive oxygen species were observed in gtpbp3 knockdown zebrafish embryos. The Gtpbp3 morphants exhibited defective in embryonic development including bleeding, melenin, oedema and curved tails within 5days post fertilization, as compared with uninjected controls. The co-injection of wild type gtpbp3 mRNA partially rescued these defects in Gtpbp3 morphants. These data suggest that zebrafish Gtpbp3 is a structural and functional homolog of human and yeast GTPBP3. The mitochondrial dysfunction caused by defective Gtpbp3 may alter the embryonic development in the zebrafish. In addition, this zebrafish model of mitochondrial disease may provide unique opportunities for studying defective tRNA modification, mitochondrial biogenesis, and pathophysiology of mitochondrial disorders.
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Affiliation(s)
- Danni Chen
- Institute of Genetics, Zhejiang University and Department of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Feng Li
- Institute of Genetics, Zhejiang University and Department of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Qingxian Yang
- Institute of Genetics, Zhejiang University and Department of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Miao Tian
- Institute of Genetics, Zhejiang University and Department of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Zengming Zhang
- Institute of Genetics, Zhejiang University and Department of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Qinghai Zhang
- Institute of Genetics, Zhejiang University and Department of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Ye Chen
- Institute of Genetics, Zhejiang University and Department of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
| | - Min-Xin Guan
- Institute of Genetics, Zhejiang University and Department of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou 310058, China; Joining Institute of Genetics and Genomic Medicine between Zhejiang University and University of Toronto, Zhejiang University, Hangzhou, Zhejiang, China.
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Gao T, Tan M, Liu W, Zhang C, Zhang T, Zheng L, Zhu J, Li L, Zhou R. GidA, a tRNA Modification Enzyme, Contributes to the Growth, and Virulence of Streptococcus suis Serotype 2. Front Cell Infect Microbiol 2016; 6:44. [PMID: 27148493 PMCID: PMC4835480 DOI: 10.3389/fcimb.2016.00044] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 03/27/2016] [Indexed: 11/16/2022] Open
Abstract
Glucose-inhibited division protein (GidA), is a tRNA modification enzyme functioning together with MnmE in the addition of a carboxymethylaminomethyl group to position 5 of the anticodon wobble uridine of tRNA. Here, we report a GidA homolog from a Chinese isolate SC-19 of the zoonotic Streptococcus suis serotype 2 (SS2). gidA disruption led to a defective growth, increased capsule thickness, and reduced hemolytic activity. Moreover, the gidA deletion mutant (ΔgidA) displayed reduced mortality and bacterial loads in mice, reduced ability of adhesion to and invasion in epithelial cells, and increased sensitivity to phagocytosis. The iTRAQ analysis identified 372 differentially expressed (182 up- and 190 down-regulated) proteins in ΔgidA and SC-19. Numerous DNA replication, cell division, and virulence associated proteins were downregulated, whereas many capsule synthesis enzymes were upregulated by gidA disruption. This is consistent with the phenotypes of the mutant. Thus, GidA is a translational regulator that plays an important role in the growth, cell division, capsule biosynthesis, and virulence of SS2. Our findings provide new insight into the regulatory function of GidA in bacterial pathogens.
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Affiliation(s)
- Ting Gao
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural UniversityWuhan, China; Veterinary Medicine Laboratory, Institute of Animal Husbandry and Veterinary Science, Hubei Academy of Agricultural ScienceWuhan, China; Wuhan Chopper Biology Co., Ltd.Wuhan, China
| | - Meifang Tan
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University Wuhan, China
| | - Wanquan Liu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University Wuhan, China
| | - Chunyan Zhang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University Wuhan, China
| | - Tengfei Zhang
- Veterinary Medicine Laboratory, Institute of Animal Husbandry and Veterinary Science, Hubei Academy of Agricultural Science Wuhan, China
| | - Linlin Zheng
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University Wuhan, China
| | - Jiawen Zhu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University Wuhan, China
| | - Lu Li
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural UniversityWuhan, China; Cooperative Innovation Center of Sustainable Pig ProductionWuhan, China
| | - Rui Zhou
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural UniversityWuhan, China; Cooperative Innovation Center of Sustainable Pig ProductionWuhan, China
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25
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Martínez-Zamora A, Meseguer S, Esteve JM, Villarroya M, Aguado C, Enríquez JA, Knecht E, Armengod ME. Defective Expression of the Mitochondrial-tRNA Modifying Enzyme GTPBP3 Triggers AMPK-Mediated Adaptive Responses Involving Complex I Assembly Factors, Uncoupling Protein 2, and the Mitochondrial Pyruvate Carrier. PLoS One 2015; 10:e0144273. [PMID: 26642043 PMCID: PMC4671719 DOI: 10.1371/journal.pone.0144273] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Accepted: 11/16/2015] [Indexed: 12/22/2022] Open
Abstract
GTPBP3 is an evolutionary conserved protein presumably involved in mitochondrial tRNA (mt-tRNA) modification. In humans, GTPBP3 mutations cause hypertrophic cardiomyopathy with lactic acidosis, and have been associated with a defect in mitochondrial translation, yet the pathomechanism remains unclear. Here we use a GTPBP3 stable-silencing model (shGTPBP3 cells) for a further characterization of the phenotype conferred by the GTPBP3 defect. We experimentally show for the first time that GTPBP3 depletion is associated with an mt-tRNA hypomodification status, as mt-tRNAs from shGTPBP3 cells were more sensitive to digestion by angiogenin than tRNAs from control cells. Despite the effect of stable silencing of GTPBP3 on global mitochondrial translation being rather mild, the steady-state levels and activity of Complex I, and cellular ATP levels were 50% of those found in the controls. Notably, the ATPase activity of Complex V increased by about 40% in GTPBP3 depleted cells suggesting that mitochondria consume ATP to maintain the membrane potential. Moreover, shGTPBP3 cells exhibited enhanced antioxidant capacity and a nearly 2-fold increase in the uncoupling protein UCP2 levels. Our data indicate that stable silencing of GTPBP3 triggers an AMPK-dependent retrograde signaling pathway that down-regulates the expression of the NDUFAF3 and NDUFAF4 Complex I assembly factors and the mitochondrial pyruvate carrier (MPC), while up-regulating the expression of UCP2. We also found that genes involved in glycolysis and oxidation of fatty acids are up-regulated. These data are compatible with a model in which high UCP2 levels, together with a reduction in pyruvate transport due to the down-regulation of MPC, promote a shift from pyruvate to fatty acid oxidation, and to an uncoupling of glycolysis and oxidative phosphorylation. These metabolic alterations, and the low ATP levels, may negatively affect heart function.
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Affiliation(s)
- Ana Martínez-Zamora
- Laboratory of RNA Modification and Mitochondrial Diseases, Centro de Investigación Príncipe Felipe, Valencia, Spain
| | - Salvador Meseguer
- Laboratory of RNA Modification and Mitochondrial Diseases, Centro de Investigación Príncipe Felipe, Valencia, Spain
| | - Juan M. Esteve
- Laboratory of Intracellular Protein Degradation and Rare Diseases, Centro de Investigación Príncipe Felipe, Valencia, Spain
| | - Magda Villarroya
- Laboratory of RNA Modification and Mitochondrial Diseases, Centro de Investigación Príncipe Felipe, Valencia, Spain
| | - Carmen Aguado
- Laboratory of Intracellular Protein Degradation and Rare Diseases, Centro de Investigación Príncipe Felipe, Valencia, Spain
- Centro de Investigación Biomédica En Red de Enfermedades Raras (CIBERER), node U721, Valencia, Spain
| | - J. Antonio Enríquez
- Departamento de Desarrollo y Reparación Cardiovascular, Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain
| | - Erwin Knecht
- Laboratory of Intracellular Protein Degradation and Rare Diseases, Centro de Investigación Príncipe Felipe, Valencia, Spain
- Centro de Investigación Biomédica En Red de Enfermedades Raras (CIBERER), node U721, Valencia, Spain
| | - M.-Eugenia Armengod
- Laboratory of RNA Modification and Mitochondrial Diseases, Centro de Investigación Príncipe Felipe, Valencia, Spain
- Centro de Investigación Biomédica En Red de Enfermedades Raras (CIBERER), node U721, Valencia, Spain
- * E-mail:
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Armengod ME, Meseguer S, Villarroya M, Prado S, Moukadiri I, Ruiz-Partida R, Garzón MJ, Navarro-González C, Martínez-Zamora A. Modification of the wobble uridine in bacterial and mitochondrial tRNAs reading NNA/NNG triplets of 2-codon boxes. RNA Biol 2015; 11:1495-507. [PMID: 25607529 DOI: 10.4161/15476286.2014.992269] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Posttranscriptional modification of the uridine located at the wobble position (U34) of tRNAs is crucial for optimization of translation. Defects in the U34 modification of mitochondrial-tRNAs are associated with a group of rare diseases collectively characterized by the impairment of the oxidative phosphorylation system. Retrograde signaling pathways from mitochondria to nucleus are involved in the pathophysiology of these diseases. These pathways may be triggered by not only the disturbance of the mitochondrial (mt) translation caused by hypomodification of tRNAs, but also as a result of nonconventional roles of mt-tRNAs and mt-tRNA-modifying enzymes. The evolutionary conservation of these enzymes supports their importance for cell and organismal functions. Interestingly, bacterial and eukaryotic cells respond to stress by altering the expression or activity of these tRNA-modifying enzymes, which leads to changes in the modification status of tRNAs. This review summarizes recent findings about these enzymes and sets them within the previous data context.
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Affiliation(s)
- M Eugenia Armengod
- a Laboratory of RNA Modification and Mitochondrial Diseases ; Centro de Investigación Príncipe Felipe ; Valencia , Spain
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Abstract
Transfer RNA (tRNA) from all organisms on this planet contains modified nucleosides, which are derivatives of the four major nucleosides. tRNA from Escherichia coli/Salmonella enterica contains 31 different modified nucleosides, which are all, except for one (Queuosine[Q]), synthesized on an oligonucleotide precursor, which through specific enzymes later matures into tRNA. The corresponding structural genes for these enzymes are found in mono- and polycistronic operons, the latter of which have a complex transcription and translation pattern. The syntheses of some of them (e.g.,several methylated derivatives) are catalyzed by one enzyme, which is position and base specific, but synthesis of some have a very complex biosynthetic pathway involving several enzymes (e.g., 2-thiouridines, N6-threonyladenosine [t6A],and Q). Several of the modified nucleosides are essential for viability (e.g.,lysidin, t6A, 1-methylguanosine), whereas deficiency in others induces severe growth defects. However, some have no or only a small effect on growth at laboratory conditions. Modified nucleosides that are present in the anticodon loop or stem have a fundamental influence on the efficiency of charging the tRNA, reading cognate codons, and preventing missense and frameshift errors. Those, which are present in the body of the tRNA, have a primarily stabilizing effect on the tRNA. Thus, the ubiquitouspresence of these modified nucleosides plays a pivotal role in the function of the tRNA by their influence on the stability and activity of the tRNA.
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28
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Shippy DC, Fadl AA. RNA modification enzymes encoded by the gid operon: Implications in biology and virulence of bacteria. Microb Pathog 2015; 89:100-7. [PMID: 26427881 DOI: 10.1016/j.micpath.2015.09.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 09/23/2015] [Indexed: 01/10/2023]
Abstract
Ribonucleic acid (RNA) molecules consist of numerous chemically modified nucleosides that are highly conserved in eukarya, archeae, and bacteria, while others are unique to each domain of life. In bacteria, hundreds of RNA modification enzymes have been identified and implicated in biological pathways associated with many cell processes. The glucose-inhibited division (gid) operon encodes genes for two RNA modification enzymes named GidA and GidB. Studies have shown GidA is essential for the proper biosynthesis of 5-methylaminomethyl-2-thiouridine (mnm(5)s(2)U) of bacterial transfer RNA (tRNA) with GidB responsible for the methylation of the 16S ribosomal RNA (rRNA). Furthermore, deletion of gidA and gidB has shown to alter numerous bacterial properties like virulence, stress response, morphology, growth, antibiotic susceptibility, and others. In this review, we discuss the present knowledge of the RNA modification enzymes GidA and GidB, and their potential role in the biology and virulence of bacteria.
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Affiliation(s)
- Daniel C Shippy
- Department of Animal Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Amin A Fadl
- Department of Animal Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA.
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29
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Cai WM, Chionh YH, Hia F, Gu C, Kellner S, McBee ME, Ng CS, Pang YLJ, Prestwich EG, Lim KS, Babu IR, Begley TJ, Dedon PC. A Platform for Discovery and Quantification of Modified Ribonucleosides in RNA: Application to Stress-Induced Reprogramming of tRNA Modifications. Methods Enzymol 2015; 560:29-71. [PMID: 26253965 DOI: 10.1016/bs.mie.2015.03.004] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Here we describe an analytical platform for systems-level quantitative analysis of modified ribonucleosides in any RNA species, with a focus on stress-induced reprogramming of tRNA as part of a system of translational control of cell stress response. This chapter emphasizes strategies and caveats for each of the seven steps of the platform workflow: (1) RNA isolation, (2) RNA purification, (3) RNA hydrolysis to individual ribonucleosides, (4) chromatographic resolution of ribonucleosides, (5) identification of the full set of modified ribonucleosides, (6) mass spectrometric quantification of ribonucleosides, (6) interrogation of ribonucleoside datasets, and (7) mapping the location of stress-sensitive modifications in individual tRNA molecules. We have focused on the critical determinants of analytical sensitivity, specificity, precision, and accuracy in an effort to ensure the most biologically meaningful data on mechanisms of translational control of cell stress response. The methods described here should find wide use in virtually any analysis involving RNA modifications.
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Affiliation(s)
- Weiling Maggie Cai
- Department of Microbiology, National University of Singapore, Singapore; Singapore-MIT Alliance for Research and Technology, Singapore
| | - Yok Hian Chionh
- Department of Microbiology, National University of Singapore, Singapore; Singapore-MIT Alliance for Research and Technology, Singapore
| | - Fabian Hia
- Singapore-MIT Alliance for Research and Technology, Singapore
| | - Chen Gu
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Stefanie Kellner
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Megan E McBee
- Singapore-MIT Alliance for Research and Technology, Singapore; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Chee Sheng Ng
- Singapore-MIT Alliance for Research and Technology, Singapore; School of Biological Sciences, Nanyang Technological Institute, Singapore
| | - Yan Ling Joy Pang
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Erin G Prestwich
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Kok Seong Lim
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - I Ramesh Babu
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Thomas J Begley
- College of Nanoscale Engineering and Science, State University of New York, Albany, New York, USA
| | - Peter C Dedon
- Singapore-MIT Alliance for Research and Technology, Singapore; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA; Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
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30
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Gamper HB, Masuda I, Frenkel-Morgenstern M, Hou YM. The UGG Isoacceptor of tRNAPro Is Naturally Prone to Frameshifts. Int J Mol Sci 2015; 16:14866-83. [PMID: 26140378 PMCID: PMC4519876 DOI: 10.3390/ijms160714866] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 06/23/2015] [Accepted: 06/24/2015] [Indexed: 11/16/2022] Open
Abstract
Native tRNAs often contain post-transcriptional modifications to the wobble position to expand the capacity of reading the genetic code. Some of these modifications, due to the ability to confer imperfect codon-anticodon pairing at the wobble position, can induce a high propensity for tRNA to shift into alternative reading frames. An example is the native UGG isoacceptor of E. coli tRNAPro whose wobble nucleotide U34 is post-transcriptionally modified to cmo5U34 to read all four proline codons (5ʹ-CCA, 5ʹ-CCC, 5ʹ-CCG, and 5ʹ-CCU). Because the pairing of the modified anticodon to CCC codon is particularly weak relative to CCA and CCG codons, this tRNA can readily shift into both the +1 and +2-frame on the slippery mRNA sequence CCC-CG. We show that the shift to the +2-frame is more dominant, driven by the higher stability of the codon-anticodon pairing at the wobble position. Kinetic analysis suggests that both types of shifts can occur during stalling of the tRNA in a post-translocation complex or during translocation from the A to the P-site. Importantly, while the +1-frame post complex is active for peptidyl transfer, the +2-frame complex is a poor peptidyl donor. Together with our recent work, we draw a mechanistic distinction between +1 and +2-frameshifts, showing that while the +1-shifts are suppressed by the additional post-transcriptionally modified m1G37 nucleotide in the anticodon loop, the +2-shifts are suppressed by the ribosome, supporting a role of the ribosome in the overall quality control of reading-frame maintenance.
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Affiliation(s)
- Howard B Gamper
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA.
| | - Isao Masuda
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA.
| | | | - Ya-Ming Hou
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA.
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31
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Lies M, Visser BJ, Joshi MC, Magnan D, Bates D. MioC and GidA proteins promote cell division in E. coli. Front Microbiol 2015; 6:516. [PMID: 26074904 PMCID: PMC4446571 DOI: 10.3389/fmicb.2015.00516] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 05/09/2015] [Indexed: 11/24/2022] Open
Abstract
The well-conserved genes surrounding the E. coli replication origin, mioC and gidA, do not normally affect chromosome replication and have little known function. We report that mioC and gidA mutants exhibit a moderate cell division inhibition phenotype. Cell elongation is exacerbated by a fis deletion, likely owing to delayed replication and subsequent cell cycle stress. Measurements of replication initiation frequency and origin segregation indicate that mioC and gidA do not inhibit cell division through any effect on oriC function. Division inhibition is also independent of the two known replication/cell division checkpoints, SOS and nucleoid occlusion. Complementation analysis indicates that mioC and gidA affect cell division in trans, indicating their effect is at the protein level. Transcriptome analysis by RNA sequencing showed that expression of a cell division septum component, YmgF, is significantly altered in mioC and gidA mutants. Our data reveal new roles for the gene products of gidA and mioC in the division apparatus, and we propose that their expression, cyclically regulated by chromatin remodeling at oriC, is part of a cell cycle regulatory program coordinating replication initiation and cell division.
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Affiliation(s)
- Mark Lies
- Molecular and Human Genetics, Baylor College of Medicine Houston, TX, USA
| | - Bryan J Visser
- Integrative Molecular and Biomedical Sciences, Baylor College of Medicine Houston, TX, USA
| | - Mohan C Joshi
- Molecular and Human Genetics, Baylor College of Medicine Houston, TX, USA
| | - David Magnan
- Integrative Molecular and Biomedical Sciences, Baylor College of Medicine Houston, TX, USA
| | - David Bates
- Molecular and Human Genetics, Baylor College of Medicine Houston, TX, USA ; Integrative Molecular and Biomedical Sciences, Baylor College of Medicine Houston, TX, USA
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32
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Tischner C, Hofer A, Wulff V, Stepek J, Dumitru I, Becker L, Haack T, Kremer L, Datta AN, Sperl W, Floss T, Wurst W, Chrzanowska-Lightowlers Z, De Angelis MH, Klopstock T, Prokisch H, Wenz T. MTO1 mediates tissue specificity of OXPHOS defects via tRNA modification and translation optimization, which can be bypassed by dietary intervention. Hum Mol Genet 2015; 24:2247-66. [PMID: 25552653 PMCID: PMC4380071 DOI: 10.1093/hmg/ddu743] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Revised: 12/12/2014] [Accepted: 12/22/2014] [Indexed: 11/15/2022] Open
Abstract
Mitochondrial diseases often exhibit tissue-specific pathologies, but this phenomenon is poorly understood. Here we present regulation of mitochondrial translation by the Mitochondrial Translation Optimization Factor 1, MTO1, as a novel player in this scenario. We demonstrate that MTO1 mediates tRNA modification and controls mitochondrial translation rate in a highly tissue-specific manner associated with tissue-specific OXPHOS defects. Activation of mitochondrial proteases, aberrant translation products, as well as defects in OXPHOS complex assembly observed in MTO1 deficient mice further imply that MTO1 impacts translation fidelity. In our mouse model, MTO1-related OXPHOS deficiency can be bypassed by feeding a ketogenic diet. This therapeutic intervention is independent of the MTO1-mediated tRNA modification and involves balancing of mitochondrial and cellular secondary stress responses. Our results thereby establish mammalian MTO1 as a novel factor in the tissue-specific regulation of OXPHOS and fine tuning of mitochondrial translation accuracy.
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Affiliation(s)
- Christin Tischner
- Institute for Genetics and Cluster of Excellence: Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Zülpicher Str. 47A, Cologne 50674, Germany
| | - Annette Hofer
- Institute for Genetics and Cluster of Excellence: Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Zülpicher Str. 47A, Cologne 50674, Germany
| | - Veronika Wulff
- Institute for Genetics and Cluster of Excellence: Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Zülpicher Str. 47A, Cologne 50674, Germany
| | - Joanna Stepek
- Institute for Genetics and Cluster of Excellence: Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Zülpicher Str. 47A, Cologne 50674, Germany
| | - Iulia Dumitru
- Institute for Genetics and Cluster of Excellence: Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Zülpicher Str. 47A, Cologne 50674, Germany
| | - Lore Becker
- Department of Neurology, Friedrich-Baur-Institute, Ludwig-Maximilians-University, Munich 80336, Germany, German Mouse Clinic, Institute of Experimental Genetics
| | - Tobias Haack
- Institute of Human Genetics, German Network for Mitochondrial Disorders (mitoNET), Germany
| | - Laura Kremer
- Institute of Human Genetics, German Network for Mitochondrial Disorders (mitoNET), Germany
| | - Alexandre N Datta
- Division of Neuropediatrics and Developmental Medicine, University Children's Hospital Basel (UKBB), University of Basel, Basel 4031, Switzerland
| | - Wolfgang Sperl
- German Network for Mitochondrial Disorders (mitoNET), Germany, Department of Pediatrics, Paracelsus Medical University Salzburg, Salzburg, Austria
| | - Thomas Floss
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environment and Health (GmbH), Neuherberg 85764, Germany
| | - Wolfgang Wurst
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environment and Health (GmbH), Neuherberg 85764, Germany, Technical University Munich, Helmholtz Zentrum München, Neuherberg 85764, Germany, DZNE-German Center for Neurodegenerative Diseases, Munich, Germany, Max Planck Institute of Psychiatry, Munich 80804, Germany, German Center for Vertigo and Balance Disorders, Munich, Germany
| | - Zofia Chrzanowska-Lightowlers
- The Wellcome Trust Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, The Medical School, Newcastle upon Tyne NE2 4HH, UK
| | - Martin Hrabe De Angelis
- German Mouse Clinic, Institute of Experimental Genetics, German Center for Vertigo and Balance Disorders, Munich, Germany, Center of Life and Food Sciences Weihenstephan, Technische Universitat München, Freising 85350, Germany, German Center for Diabetes Research (DZD), Neuherberg 85764, Germany and Technische Universität München, Freising-Weihenstephan 85354, Germany
| | - Thomas Klopstock
- Department of Neurology, Friedrich-Baur-Institute, Ludwig-Maximilians-University, Munich 80336, Germany, German Mouse Clinic, Institute of Experimental Genetics, German Network for Mitochondrial Disorders (mitoNET), Germany, DZNE-German Center for Neurodegenerative Diseases, Munich, Germany, German Center for Vertigo and Balance Disorders, Munich, Germany
| | - Holger Prokisch
- Institute of Human Genetics, Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environment and Health (GmbH), Neuherberg 85764, Germany
| | - Tina Wenz
- Institute for Genetics and Cluster of Excellence: Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Zülpicher Str. 47A, Cologne 50674, Germany, German Network for Mitochondrial Disorders (mitoNET), Germany,
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33
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Krasich R, Wu SY, Kuo HK, Kreuzer KN. Functions that protect Escherichia coli from DNA-protein crosslinks. DNA Repair (Amst) 2015; 28:48-59. [PMID: 25731940 DOI: 10.1016/j.dnarep.2015.01.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Revised: 01/27/2015] [Accepted: 01/30/2015] [Indexed: 10/24/2022]
Abstract
Pathways for tolerating and repairing DNA-protein crosslinks (DPCs) are poorly defined. We used transposon mutagenesis and candidate gene approaches to identify DPC-hypersensitive Escherichia coli mutants. DPCs were induced by azacytidine (aza-C) treatment in cells overexpressing cytosine methyltransferase; hypersensitivity was verified to depend on methyltransferase expression. We isolated hypersensitive mutants that were uncovered in previous studies (recA, recBC, recG, and uvrD), hypersensitive mutants that apparently activate phage Mu Gam expression, and novel hypersensitive mutants in genes involved in DNA metabolism, cell division, and tRNA modification (dinG, ftsK, xerD, dnaJ, hflC, miaA, mnmE, mnmG, and ssrA). Inactivation of SbcCD, which can cleave DNA at protein-DNA complexes, did not cause hypersensitivity. We previously showed that tmRNA pathway defects cause aza-C hypersensitivity, implying that DPCs block coupled transcription/translation complexes. Here, we show that mutants in tRNA modification functions miaA, mnmE and mnmG cause defects in aza-C-induced tmRNA tagging, explaining their hypersensitivity. In order for tmRNA to access a stalled ribosome, the mRNA must be cleaved or released from RNA polymerase. Mutational inactivation of functions involved in mRNA processing and RNA polymerase elongation/release (RNase II, RNaseD, RNase PH, RNase LS, Rep, HepA, GreA, GreB) did not cause aza-C hypersensitivity; the mechanism of tmRNA access remains unclear.
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Affiliation(s)
- Rachel Krasich
- Department of Biochemistry, Duke University Medical Center, Durham NC 27710, United States
| | - Sunny Yang Wu
- Department of Biochemistry, Duke University Medical Center, Durham NC 27710, United States
| | - H Kenny Kuo
- Department of Biochemistry, Duke University Medical Center, Durham NC 27710, United States
| | - Kenneth N Kreuzer
- Department of Biochemistry, Duke University Medical Center, Durham NC 27710, United States.
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Ragionieri L, Vitorino R, Frommlet J, Oliveira JL, Gaspar P, Ribas de Pouplana L, Santos MAS, Moura GR. Improving the accuracy of recombinant protein production through integration of bioinformatics, statistical and mass spectrometry methodologies. FEBS J 2015; 282:769-87. [DOI: 10.1111/febs.13181] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Revised: 10/09/2014] [Accepted: 12/16/2014] [Indexed: 02/05/2023]
Affiliation(s)
- Lapo Ragionieri
- RNA and Genome Biology Laboratories; Department of Biology/Health Sciences; Centro de Estudos do Ambiente e do Mar iBiMED; University of Aveiro; Portugal
| | - Rui Vitorino
- Department of Chemistry; University of Aveiro; Portugal
| | - Joerg Frommlet
- Department of Biology and Centro de Estudos do Ambiente e do Mar; University of Aveiro; Portugal
| | - José L. Oliveira
- Department of Electronics; Telecommunications and Informatics and Instituto de Engenharia Electrónica e Telemática de Aveiro; University of Aveiro; Portugal
| | - Paulo Gaspar
- Department of Electronics; Telecommunications and Informatics and Instituto de Engenharia Electrónica e Telemática de Aveiro; University of Aveiro; Portugal
| | - Lluís Ribas de Pouplana
- Institute for Research in Biomedicine; Barcelona Spain
- Catalan Institution for Research and Advanced Studies; Barcelona Spain
| | - Manuel A. Silva Santos
- RNA and Genome Biology Laboratories; Department of Biology/Health Sciences; Centro de Estudos do Ambiente e do Mar iBiMED; University of Aveiro; Portugal
| | - Gabriela Ribeiro Moura
- RNA and Genome Biology Laboratories; Department of Biology/Health Sciences; Centro de Estudos do Ambiente e do Mar iBiMED; University of Aveiro; Portugal
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35
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Petersen LM, Tisa LS. Molecular characterization of protease activity in Serratia sp. strain SCBI and its importance in cytotoxicity and virulence. J Bacteriol 2014; 196:3923-36. [PMID: 25182493 PMCID: PMC4248818 DOI: 10.1128/jb.01908-14] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Accepted: 08/26/2014] [Indexed: 01/19/2023] Open
Abstract
A newly recognized Serratia species, termed South African Caenorhabditis briggsae isolate (SCBI), is both a mutualist of the nematode Caenorhabditis briggsae KT0001 and a pathogen of lepidopteran insects. Serratia sp. strain SCBI displays high proteolytic activity, and because secreted proteases are known virulence factors for many pathogens, the purpose of this study was to identify genes essential for extracellular protease activity in Serratia sp. strain SCBI and to determine what role proteases play in insect pathogenesis and cytotoxicity. A bank of 2,100 transposon mutants was generated, and six SCBI mutants with defective proteolytic activity were identified. These mutants were also defective in cytotoxicity. The mutants were found defective in genes encoding the following proteins: alkaline metalloprotease secretion protein AprE, a BglB family transcriptional antiterminator, an inosine/xanthosine triphosphatase, GidA, a methyl-accepting chemotaxis protein, and a PIN domain protein. Gene expression analysis on these six mutants showed significant downregulation in mRNA levels of several different types of predicted protease genes. In addition, transcriptome sequencing (RNA-seq) analysis provided insight into how inactivation of AprE, GidA, and a PIN domain protein influences motility and virulence, as well as protease activity. Using quantitative reverse transcription-PCR (qRT-PCR) to further characterize expression of predicted protease genes in wild-type Serratia sp. SCBI, the highest mRNA levels for the alkaline metalloprotease genes (termed prtA1 to prtA4) occurred following the death of an insect host, while two serine protease and two metalloprotease genes had their highest mRNA levels during active infection. Overall, these results indicate that proteolytic activity is essential for cytotoxicity in Serratia sp. SCBI and that its regulation appears to be highly complex.
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Affiliation(s)
- Lauren M Petersen
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, USA
| | - Louis S Tisa
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, USA
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36
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tRNA modification enzymes GidA and MnmE: potential role in virulence of bacterial pathogens. Int J Mol Sci 2014; 15:18267-80. [PMID: 25310651 PMCID: PMC4227215 DOI: 10.3390/ijms151018267] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Revised: 10/02/2014] [Accepted: 10/08/2014] [Indexed: 01/02/2023] Open
Abstract
Transfer RNA (tRNA) is an RNA molecule that carries amino acids to the ribosomes for protein synthesis. These tRNAs function at the peptidyl (P) and aminoacyl (A) binding sites of the ribosome during translation, with each codon being recognized by a specific tRNA. Due to this specificity, tRNA modification is essential for translational efficiency. Many enzymes have been implicated in the modification of bacterial tRNAs, and these enzymes may complex with one another or interact individually with the tRNA. Approximately, 100 tRNA modification enzymes have been identified with glucose-inhibited division (GidA) protein and MnmE being two of the enzymes studied. In Escherichia coli and Salmonella, GidA and MnmE bind together to form a functional complex responsible for the proper biosynthesis of 5-methylaminomethyl-2-thiouridine (mnm5s2U34) of tRNAs. Studies have implicated this pathway in a major pathogenic regulatory mechanism as deletion of gidA and/or mnmE has attenuated several bacterial pathogens like Salmonella enterica serovar Typhimurium, Pseudomonas syringae, Aeromonas hydrophila, and many others. In this review, we summarize the potential role of the GidA/MnmE tRNA modification pathway in bacterial virulence, interactions with the host, and potential therapeutic strategies resulting from a greater understanding of this regulatory mechanism.
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Meseguer S, Martínez-Zamora A, García-Arumí E, Andreu AL, Armengod ME. The ROS-sensitive microRNA-9/9* controls the expression of mitochondrial tRNA-modifying enzymes and is involved in the molecular mechanism of MELAS syndrome. Hum Mol Genet 2014; 24:167-84. [PMID: 25149473 DOI: 10.1093/hmg/ddu427] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Mitochondrial dysfunction activates mitochondria-to-nucleus signaling pathways whose components are mostly unknown. Identification of these components is important to understand the molecular mechanisms underlying mitochondrial diseases and to discover putative therapeutic targets. MELAS syndrome is a rare neurodegenerative disease caused by mutations in mitochondrial (mt) DNA affecting mt-tRNA(Leu(UUR)). Patient and cybrid cells exhibit elevated oxidative stress. Moreover, mutant mt-tRNAs(Leu(UUR)) lack the taurine-containing modification normally present at the wobble uridine (U34) of wild-type mt-tRNA(Leu(UUR)), which is considered an etiology of MELAS. However, the molecular mechanism is still unclear. We found that MELAS cybrids exhibit a significant decrease in the steady-state levels of several mt-tRNA-modification enzymes, which is not due to transcriptional regulation. We demonstrated that oxidative stress mediates an NFkB-dependent induction of microRNA-9/9*, which acts as a post-transcriptional negative regulator of the mt-tRNA-modification enzymes GTPBP3, MTO1 and TRMU. Down-regulation of these enzymes by microRNA-9/9* affects the U34 modification status of non-mutant tRNAs and contributes to the MELAS phenotype. Anti-microRNA-9 treatments of MELAS cybrids reverse the phenotype, whereas miR-9 transfection of wild-type cells mimics the effects of siRNA-mediated down-regulation of GTPBP3, MTO1 and TRMU. Our data represent the first evidence that an mt-DNA disease can directly affect microRNA expression. Moreover, we demonstrate that the modification status of mt-tRNAs is dynamic and that cells respond to stress by modulating the expression of mt-tRNA-modifying enzymes. microRNA-9/9* is a crucial player in mitochondria-to-nucleus signaling as it regulates expression of nuclear genes in response to changes in the functional state of mitochondria.
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Affiliation(s)
- Salvador Meseguer
- Laboratory of RNA Modification and Mitochondrial Diseases, Centro de Investigación Príncipe Felipe, Valencia 46012, Spain
| | - Ana Martínez-Zamora
- Laboratory of RNA Modification and Mitochondrial Diseases, Centro de Investigación Príncipe Felipe, Valencia 46012, Spain
| | - Elena García-Arumí
- Hospital Universitari Vall d'Hebron, Institut de Recerca, Universitat Autònoma de Barcelona, Barcelona 08035, Spain Biomedical Research Networking Centre for Rare Diseases (CIBERER) (node U701), Barcelona, Spain and
| | - Antonio L Andreu
- Hospital Universitari Vall d'Hebron, Institut de Recerca, Universitat Autònoma de Barcelona, Barcelona 08035, Spain Biomedical Research Networking Centre for Rare Diseases (CIBERER) (node U701), Barcelona, Spain and
| | - M-Eugenia Armengod
- Laboratory of RNA Modification and Mitochondrial Diseases, Centro de Investigación Príncipe Felipe, Valencia 46012, Spain CIBERER (node U721), Valencia, Spain
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Björk GR, Hagervall TG. Transfer RNA Modification: Presence, Synthesis, and Function. EcoSal Plus 2014; 6. [PMID: 26442937 DOI: 10.1128/ecosalplus.esp-0007-2013] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Indexed: 06/05/2023]
Abstract
Transfer RNA (tRNA) from all organisms on this planet contains modified nucleosides, which are derivatives of the four major nucleosides. tRNA from Escherichia coli/Salmonella enterica serovar Typhimurium contains 33 different modified nucleosides, which are all, except one (Queuosine [Q]), synthesized on an oligonucleotide precursor, which by specific enzymes later matures into tRNA. The structural genes for these enzymes are found in mono- and polycistronic operons, the latter of which have a complex transcription and translation pattern. The synthesis of the tRNA-modifying enzymes is not regulated similarly, and it is not coordinated to that of their substrate, the tRNA. The synthesis of some of them (e.g., several methylated derivatives) is catalyzed by one enzyme, which is position and base specific, whereas synthesis of some has a very complex biosynthetic pathway involving several enzymes (e.g., 2-thiouridines, N 6-cyclicthreonyladenosine [ct6A], and Q). Several of the modified nucleosides are essential for viability (e.g., lysidin, ct6A, 1-methylguanosine), whereas the deficiency of others induces severe growth defects. However, some have no or only a small effect on growth at laboratory conditions. Modified nucleosides that are present in the anticodon loop or stem have a fundamental influence on the efficiency of charging the tRNA, reading cognate codons, and preventing missense and frameshift errors. Those that are present in the body of the tRNA primarily have a stabilizing effect on the tRNA. Thus, the ubiquitous presence of these modified nucleosides plays a pivotal role in the function of the tRNA by their influence on the stability and activity of the tRNA.
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Affiliation(s)
- Glenn R Björk
- Department of Molecular Biology, Umeå University, S-90187 Umeå, Sweden
| | - Tord G Hagervall
- Department of Molecular Biology, Umeå University, S-90187 Umeå, Sweden
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39
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Zhou Q, Wang W, He X, Zhu X, Shen Y, Yu Z, Wang X, Qi X, Zhang X, Fan M, Dai Y, Yang S, Yan Q. Mechanistic study on the nuclear modifier gene MSS1 mutation suppressing neomycin sensitivity of the mitochondrial 15S rRNA C1477G mutation in Saccharomyces cerevisiae. PLoS One 2014; 9:e90336. [PMID: 24595024 PMCID: PMC3940847 DOI: 10.1371/journal.pone.0090336] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Accepted: 01/30/2014] [Indexed: 12/31/2022] Open
Abstract
The phenotypic manifestation of mitochondrial DNA (mtDNA) mutations can be modulated by nuclear genes and environmental factors. However, neither the interaction among these factors nor their underlying mechanisms are well understood. The yeast Saccharomyces cerevisiae mtDNA 15S rRNA C1477G mutation (PR) corresponds to the human 12S rRNA A1555G mutation. Here we report that a nuclear modifier gene mss1 mutation suppresses the neomycin-sensitivity phenotype of a yeast C1477G mutant in fermentable YPD medium. Functional assays show that the mitochondrial function of the yeast C1477G mutant was impaired severely in YPD medium with neomycin. Moreover, the mss1 mutation led to a significant increase in the steady-state level of HAP5 (heme activated protein), which greatly up-regulated the expression of glycolytic transcription factors RAP1, GCR1, and GCR2 and thus stimulated glycolysis. Furthermore, the high expression of the key glycolytic enzyme genes HXK2, PFK1 and PYK1 indicated that enhanced glycolysis not only compensated for the ATP reduction from oxidative phosphorylation (OXPHOS) in mitochondria, but also ensured the growth of the mss1(PR) mutant in YPD medium with neomycin. This study advances our understanding of the phenotypic manifestation of mtDNA mutations.
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Affiliation(s)
- Qiyin Zhou
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Wei Wang
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Xiangyu He
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Xiaoyu Zhu
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Yaoyao Shen
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Zhe Yu
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Xuexiang Wang
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Xuchen Qi
- Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xuan Zhang
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Mingjie Fan
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Yu Dai
- College of Life Sciences, Zhejiang University, Hangzhou, China
- The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Shuxu Yang
- Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Qingfeng Yan
- College of Life Sciences, Zhejiang University, Hangzhou, China
- * E-mail:
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40
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Posttranscriptional RNA Modifications: playing metabolic games in a cell's chemical Legoland. ACTA ACUST UNITED AC 2013; 21:174-85. [PMID: 24315934 DOI: 10.1016/j.chembiol.2013.10.015] [Citation(s) in RCA: 164] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Revised: 10/24/2013] [Accepted: 10/30/2013] [Indexed: 12/15/2022]
Abstract
Nature combines existing biochemical building blocks, at times with subtlety of purpose. RNA modifications are a prime example of this, where standard RNA nucleosides are decorated with chemical groups and building blocks that we recall from our basic biochemistry lectures. The result: a wealth of chemical diversity whose full biological relevance has remained elusive despite being public knowledge for some time. Here, we highlight several modifications that, because of their chemical intricacy, rely on seemingly unrelated pathways to provide cofactors for their synthesis. Besides their immediate role in affecting RNA function, modifications may act as sensors and transducers of information that connect a cell's metabolic state to its translational output, carefully orchestrating a delicate balance between metabolic rate and protein synthesis at a system's level.
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41
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Moukadiri I, Garzón MJ, Björk GR, Armengod ME. The output of the tRNA modification pathways controlled by the Escherichia coli MnmEG and MnmC enzymes depends on the growth conditions and the tRNA species. Nucleic Acids Res 2013; 42:2602-23. [PMID: 24293650 PMCID: PMC3936742 DOI: 10.1093/nar/gkt1228] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
In Escherichia coli, the MnmEG complex modifies transfer RNAs (tRNAs) decoding NNA/NNG codons. MnmEG catalyzes two different modification reactions, which add an aminomethyl (nm) or carboxymethylaminomethyl (cmnm) group to position 5 of the anticodon wobble uridine using ammonium or glycine, respectively. In and , however, cmnm5 appears as the final modification, whereas in the remaining tRNAs, the MnmEG products are converted into 5-methylaminomethyl (mnm5) through the two-domain, bi-functional enzyme MnmC. MnmC(o) transforms cmnm5 into nm5, whereas MnmC(m) converts nm5 into mnm5, thus producing an atypical network of modification pathways. We investigate the activities and tRNA specificity of MnmEG and the MnmC domains, the ability of tRNAs to follow the ammonium or glycine pathway and the effect of mnmC mutations on growth. We demonstrate that the two MnmC domains function independently of each other and that and are substrates for MnmC(m), but not MnmC(o). Synthesis of mnm5s2U by MnmEG-MnmC in vivo avoids build-up of intermediates in . We also show that MnmEG can modify all the tRNAs via the ammonium pathway. Strikingly, the net output of the MnmEG pathways in vivo depends on growth conditions and tRNA species. Loss of any MnmC activity has a biological cost under specific conditions.
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Affiliation(s)
- Ismaïl Moukadiri
- Laboratory of RNA Modification and Mitochondrial Diseases, Príncipe Felipe Research Center, 46012-Valencia, Spain, Department of Molecular Biology, Umeå University, S90187, Sweden and Biomedical Research Networking Centre for Rare Diseases (CIBERER) (node U721), Spain
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42
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Baldridge KC, Contreras LM. Functional implications of ribosomal RNA methylation in response to environmental stress. Crit Rev Biochem Mol Biol 2013; 49:69-89. [PMID: 24261569 DOI: 10.3109/10409238.2013.859229] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The study of post-transcriptional RNA modifications has long been focused on the roles these chemical modifications play in maintaining ribosomal function. The field of ribosomal RNA modification has reached a milestone in recent years with the confirmation of the final unknown ribosomal RNA methyltransferase in Escherichia coli in 2012. Furthermore, the last 10 years have brought numerous discoveries in non-coding RNAs and the roles that post-transcriptional modification play in their functions. These observations indicate the need for a revitalization of this field of research to understand the role modifications play in maintaining cellular health in a dynamic environment. With the advent of high-throughput sequencing technologies, the time is ripe for leaps and bounds forward. This review discusses ribosomal RNA methyltransferases and their role in responding to external stress in Escherichia coli, with a specific focus on knockout studies and on analysis of transcriptome data with respect to rRNA methyltransferases.
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Affiliation(s)
- Kevin C Baldridge
- McKetta Department of Chemical Engineering, The University of Texas at Austin , Austin, TX , USA
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43
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Green AJ, Alaulamie AA, Baral S, Richardson HH. Ultrasensitive molecular detection using thermal conductance of a hydrophobic gold-water interface. NANO LETTERS 2013; 13:4142-4147. [PMID: 23924145 DOI: 10.1021/nl401717y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The thermal conductance from a hydrophobic gold aqueous interface is measured with increasing solute concentration. A small amount of aqueous solute molecules (1 solute molecule in 550 water molecules) dramatically increases the heat dissipation into the surrounding liquid. This result is consistent with a thermal conductance that is limited by an interface interaction where minority aqueous components significantly alter the surface properties and heat transport through the interface. The increase in heat dissipation can be used to make an extremely sensitive molecular detector that can be scaled to give single molecule detection without amplification or utilizing fluorescence labels.
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Affiliation(s)
- Andrew J Green
- Department of Chemistry and Biochemistry, Ohio University , Athens, Ohio 45701, United States
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44
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Swinehart WE, Henderson JC, Jackman JE. Unexpected expansion of tRNA substrate recognition by the yeast m1G9 methyltransferase Trm10. RNA (NEW YORK, N.Y.) 2013; 19:1137-46. [PMID: 23793893 PMCID: PMC3708533 DOI: 10.1261/rna.039651.113] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
N-1 Methylation of the nearly invariant purine residue found at position 9 of tRNA is a nucleotide modification found in multiple tRNA species throughout Eukarya and Archaea. First discovered in Saccharomyces cerevisiae, the tRNA methyltransferase Trm10 is a highly conserved protein both necessary and sufficient to catalyze all known instances of m1G9 modification in yeast. Although there are 19 unique tRNA species that contain a G at position 9 in yeast, and whose fully modified sequence is known, only 9 of these tRNA species are modified with m1G9 in wild-type cells. The elements that allow Trm10 to distinguish between structurally similar tRNA species are not known, and sequences that are shared between all substrate or all nonsubstrate tRNAs have not been identified. Here, we demonstrate that the in vitro methylation activity of yeast Trm10 is not sufficient to explain the observed pattern of modification in vivo, as additional tRNA species are substrates for Trm10 m1G9 methyltransferase activity. Similarly, overexpression of Trm10 in yeast yields m1G9 containing tRNA species that are ordinarily unmodified in vivo. Thus, yeast Trm10 has a significantly broader tRNA substrate specificity than is suggested by the observed pattern of modification in wild-type yeast. These results may shed light onto the suggested involvement of Trm10 in other pathways in other organisms, particularly in higher eukaryotes that contain up to three different genes with sequence similarity to the single TRM10 gene in yeast, and where these other enzymes have been implicated in pathways beyond tRNA processing.
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MESH Headings
- Genes, Fungal
- Guanosine/analogs & derivatives
- Guanosine/chemistry
- Humans
- Kinetics
- Methylation
- RNA Processing, Post-Transcriptional
- RNA, Fungal/chemistry
- RNA, Fungal/metabolism
- RNA, Transfer/chemistry
- RNA, Transfer/metabolism
- RNA, Transfer, Val/chemistry
- RNA, Transfer, Val/metabolism
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae/metabolism
- Saccharomyces cerevisiae Proteins/genetics
- Saccharomyces cerevisiae Proteins/metabolism
- Substrate Specificity
- tRNA Methyltransferases/genetics
- tRNA Methyltransferases/metabolism
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Affiliation(s)
- William E. Swinehart
- Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, USA
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
- Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio 43210, USA
| | - Jeremy C. Henderson
- Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, USA
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Jane E. Jackman
- Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, USA
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
- Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio 43210, USA
- Corresponding authorE-mail
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45
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Prado S, Villarroya M, Medina M, Armengod ME. The tRNA-modifying function of MnmE is controlled by post-hydrolysis steps of its GTPase cycle. Nucleic Acids Res 2013; 41:6190-208. [PMID: 23630314 PMCID: PMC3695501 DOI: 10.1093/nar/gkt320] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
MnmE is a homodimeric multi-domain GTPase involved in tRNA modification. This protein differs from Ras-like GTPases in its low affinity for guanine nucleotides and mechanism of activation, which occurs by a cis, nucleotide- and potassium-dependent dimerization of its G-domains. Moreover, MnmE requires GTP hydrolysis to be functionally active. However, how GTP hydrolysis drives tRNA modification and how the MnmE GTPase cycle is regulated remains unresolved. Here, the kinetics of the MnmE GTPase cycle was studied under single-turnover conditions using stopped- and quench-flow techniques. We found that the G-domain dissociation is the rate-limiting step of the overall reaction. Mutational analysis and fast kinetics assays revealed that GTP hydrolysis, G-domain dissociation and Pi release can be uncoupled and that G-domain dissociation is directly responsible for the ‘ON’ state of MnmE. Thus, MnmE provides a new paradigm of how the ON/OFF cycling of GTPases may regulate a cellular process. We also demonstrate that the MnmE GTPase cycle is negatively controlled by the reaction products GDP and Pi. This feedback mechanism may prevent inefficacious GTP hydrolysis in vivo. We propose a biological model whereby a conformational change triggered by tRNA binding is required to remove product inhibition and initiate a new GTPase/tRNA-modification cycle.
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Affiliation(s)
- Silvia Prado
- RNA Modification and Mitochondrial Diseases Laboratory, Centro de Investigación Príncipe Felipe, 46012-Valencia, Spain
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46
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GidA Expression in Salmonella is Modulated Under Certain Environmental Conditions. Curr Microbiol 2013; 67:279-85. [DOI: 10.1007/s00284-013-0361-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2012] [Accepted: 02/26/2013] [Indexed: 01/03/2023]
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47
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Shippy DC, Eakley NM, Lauhon CT, Bochsler PN, Fadl AA. Virulence characteristics of Salmonella following deletion of genes encoding the tRNA modification enzymes GidA and MnmE. Microb Pathog 2013; 57:1-9. [DOI: 10.1016/j.micpath.2013.01.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2012] [Revised: 01/11/2013] [Accepted: 01/14/2013] [Indexed: 12/25/2022]
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48
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Luo LF, Hou CC, Yang WX. Nuclear factors: roles related to mitochondrial deafness. Gene 2013; 520:79-89. [PMID: 23510774 DOI: 10.1016/j.gene.2013.03.041] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Accepted: 03/08/2013] [Indexed: 12/16/2022]
Abstract
Hearing loss (HL) is a common disorder with mitochondrial dysfunction as one of the major causes leading to deafness. Mitochondrial dysfunction may be caused by either mutations in nuclear genes leading to defective nuclear-encoded proteins or mutations in mitochondrial genes leading to defective mitochondrial-encoded products. The specific nuclear genes involved in HL can be classified into two categories depending on whether mitochondrial gene mutations co-exist (modifier genes) or not (deafness-causing genes). TFB1M, MTO1, GTPBP3, and TRMU are modifier genes. A mutation in any of these modifier genes may lead to a deafness phenotype when accompanied by the mitochondrial gene mutation. OPA1, TIMM8A, SMAC/DIABLO, MPV17, PDSS1, BCS1L, SUCLA2, C10ORF2, COX10, PLOG1and RRM2B are deafness-causing genes. A mutation in any of these deafness-causing genes will directly induce variable phenotypic HL.
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Affiliation(s)
- Ling-Feng Luo
- Institute of Cell and Developmental Biology, Zhejiang University, Hangzhou 310058, China
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Zhou W, Karcher D, Bock R. Importance of adenosine-to-inosine editing adjacent to the anticodon in an Arabidopsis alanine tRNA under environmental stress. Nucleic Acids Res 2013; 41:3362-72. [PMID: 23355609 PMCID: PMC3597679 DOI: 10.1093/nar/gkt013] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In all organisms, transfer RNAs (tRNAs) undergo extensive post-transcriptional modifications. Although base modifications in the anticodon are known to alter decoding specificity or improve decoding accuracy, much less is known about the functional relevance of modifications in other positions of tRNAs. Here, we report the identification of an A-to-I tRNA editing enzyme that modifies the tRNA-Ala(AGC) in the model plant Arabidopsis thaliana. The enzyme is homologous to Tad1p, a yeast tRNA-specific adenosine deaminase, and it selectively deaminates the adenosine in the position 3'-adjacent to the anticodon (A37) to inosine. We show that the AtTAD1 protein is exclusively localized in the nucleus. The tad1 loss-of-function mutants isolated in Arabidopsis show normal accumulation of the tRNA-Ala(AGC), suggesting that the loss of the I37 modification does not affect tRNA stability. The tad1 knockout mutants display no discernible phenotype under standard growth conditions, but produce less biomass under environmental stress conditions. Our results provide the first evidence in support of a physiological relevance of the A37-to-I modification in eukaryotes.
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Affiliation(s)
| | | | - Ralph Bock
- *To whom correspondence should be addressed. Tel: +49 3315 67 8700; Fax: +49 3315 67 8701;
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Abstract
As analytical chemists, the highest resolution measurement one can make is at the single molecule level; it just does not get any better than that. To determine the concentration of a molecule in solution, the best way is to count the number of molecules in a given volume. As long as the volume contains a statistically large enough number of molecules and is above the Poisson noise limit, molecular counting is the most accurate way to make a measurement. Molecular counting is the method of the future and is beginning to be performed today.
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Affiliation(s)
- David R Walt
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
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